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Nhàn NTT, Yamada T, Yamada KH. Peptide-Based Agents for Cancer Treatment: Current Applications and Future Directions. Int J Mol Sci 2023; 24:12931. [PMID: 37629112 PMCID: PMC10454368 DOI: 10.3390/ijms241612931] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Peptide-based strategies have received an enormous amount of attention because of their specificity and applicability. Their specificity and tumor-targeting ability are applied to diagnosis and treatment for cancer patients. In this review, we will summarize recent advancements and future perspectives on peptide-based strategies for cancer treatment. The literature search was conducted to identify relevant articles for peptide-based strategies for cancer treatment. It was performed using PubMed for articles in English until June 2023. Information on clinical trials was also obtained from ClinicalTrial.gov. Given that peptide-based strategies have several advantages such as targeted delivery to the diseased area, personalized designs, relatively small sizes, and simple production process, bioactive peptides having anti-cancer activities (anti-cancer peptides or ACPs) have been tested in pre-clinical settings and clinical trials. The capability of peptides for tumor targeting is essentially useful for peptide-drug conjugates (PDCs), diagnosis, and image-guided surgery. Immunomodulation with peptide vaccines has been extensively tested in clinical trials. Despite such advantages, FDA-approved peptide agents for solid cancer are still limited. This review will provide a detailed overview of current approaches, design strategies, routes of administration, and new technological advancements. We will highlight the success and limitations of peptide-based therapies for cancer treatment.
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Affiliation(s)
- Nguyễn Thị Thanh Nhàn
- Department of Pharmacology & Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA;
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL 60612, USA;
- Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL 60607, USA
| | - Kaori H. Yamada
- Department of Pharmacology & Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA;
- Department of Ophthalmology & Visual Sciences, University of Illinois College of Medicine, Chicago, IL 60612, USA
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2
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Abrigo NA, Dods KK, Makovsky CA, Lohan S, Mitra K, Newcomb KM, Le A, Hartman MCT. Development of a Cyclic, Cell Penetrating Peptide Compatible with In Vitro Selection Strategies. ACS Chem Biol 2023; 18:746-755. [PMID: 36920103 PMCID: PMC11165944 DOI: 10.1021/acschembio.2c00680] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A key limitation for the development of peptides as therapeutics is their lack of cell permeability. Recent work has shown that short, arginine-rich macrocyclic peptides containing hydrophobic amino acids are able to penetrate cells and reach the cytosol. Here, we have developed a new strategy for developing cyclic cell penetrating peptides (CPPs) that shifts some of the hydrophobic character to the peptide cyclization linker, allowing us to do a linker screen to find cyclic CPPs with improved cellular uptake. We demonstrate that both hydrophobicity and position of the alkylation points on the linker affect uptake of macrocyclic cell penetrating peptides (CPPs). Our best peptide, 4i, is on par with or better than prototypical CPPs Arg9 (R9) and CPP12 under assays measuring total cellular uptake and cytosolic delivery. 4i was also able to carry a peptide previously discovered from an in vitro selection, 8.6, and a cytotoxic peptide into the cytosol. A bicyclic variant of 4i showed even better cytosolic entry than 4i, highlighting the plasticity of this class of peptides toward modifications. Since our CPPs are cyclized via their side chains (as opposed to head-to-tail cyclization), they are compatible with powerful technologies for peptide ligand discovery including phage display and mRNA display. Access to diverse libraries with inherent cell permeability will afford the ability to find cell permeable hits to many challenging intracellular targets.
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Affiliation(s)
- Nicolas A Abrigo
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Kara K Dods
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Chelsea A Makovsky
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Sandeep Lohan
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Koushambi Mitra
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Kaylee M Newcomb
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Anthony Le
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
| | - Matthew C T Hartman
- Chemistry, Virginia Commonwealth University, 1001 W Main Street, Richmond, 23284 Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, 23219 Virginia, United States
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3
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Abd El-Hafeez AA, Sun N, Chakraborty A, Ear J, Roy S, Chamarthi P, Rajapakse N, Das S, Luker KE, Hazra TK, Luker GD, Ghosh P. Regulation of DNA damage response by trimeric G-proteins. iScience 2023; 26:105973. [PMID: 36756378 PMCID: PMC9900518 DOI: 10.1016/j.isci.2023.105973] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 08/14/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Upon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of the two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DSBs hinges on GIV/Girdin, a guanine nucleotide-exchange modulator of heterotrimeric Giα•βγ protein. GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1's BRCT-modules via both phospho-dependent and -independent mechanisms. Using another non-overlapping C-terminal motif GIV binds and activates Gi and enhances the "free" Gβγ→PI-3-kinase→Akt pathway, which promotes survival and is known to suppress HR, favor NHEJ. Absence of GIV, or loss of either of its C-terminal motifs enhanced cell death upon genotoxic stress. Because GIV selectively binds other BRCT-containing proteins suggests that G-proteins may fine-tune sensing, repair, and survival after diverse types of DNA damage.
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Affiliation(s)
- Amer Ali Abd El-Hafeez
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Pharmacology and Experimental Oncology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Nina Sun
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jason Ear
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, USA
| | - Suchismita Roy
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Pranavi Chamarthi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Navin Rajapakse
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Soumita Das
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Kathryn E. Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gary D. Luker
- Center for Molecular Imaging, Department of Radiology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd., Ann Arbor, MI 48109-2099, USA
- Department of Microbiology and Immunology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Comprehensive Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
- Veterans Affairs Medical Center, La Jolla, CA, USA
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4
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Nasrollahpour H, Khalilzadeh B, Hasanzadeh M, Rahbarghazi R, Estrela P, Naseri A, Tasoglu S, Sillanpää M. Nanotechnology‐based electrochemical biosensors for monitoring breast cancer biomarkers. Med Res Rev 2022; 43:464-569. [PMID: 36464910 DOI: 10.1002/med.21931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 10/01/2022] [Accepted: 11/04/2022] [Indexed: 12/07/2022]
Abstract
Breast cancer is categorized as the most widespread cancer type among women globally. On-time diagnosis can decrease the mortality rate by making the right decision in the therapy procedure. These features lead to a reduction in medication time and socioeconomic burden. The current review article provides a comprehensive assessment for breast cancer diagnosis using nanomaterials and related technologies. Growing use of the nano/biotechnology domain in terms of electrochemical nanobiosensor designing was discussed in detail. In this regard, recent advances in nanomaterial applied for amplified biosensing methodologies were assessed for breast cancer diagnosis by focusing on the advantages and disadvantages of these approaches. We also monitored designing methods, advantages, and the necessity of suitable (nano) materials from a statistical standpoint. The main objective of this review is to classify the applicable biosensors based on breast cancer biomarkers. With numerous nano-sized platforms published for breast cancer diagnosis, this review tried to collect the most suitable methodologies for detecting biomarkers and certain breast cancer cell types.
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Affiliation(s)
- Hassan Nasrollahpour
- Department of Analytical Chemistry, Faculty of Chemistry University of Tabriz Tabriz Iran
| | - Balal Khalilzadeh
- Stem Cell Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center Tabriz University of Medical Sciences Tabriz Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Applied Cellular Sciences, Faculty of Advanced Medical Sciences Tabriz University of Medical Sciences Tabriz Iran
| | - Pedro Estrela
- Centre for Biosensors, Bioelectronics and Biodevices (C3Bio) and Department of Electronic and Electrical Engineering University of Bath Bath UK
| | - Abdolhossein Naseri
- Department of Analytical Chemistry, Faculty of Chemistry University of Tabriz Tabriz Iran
| | - Savas Tasoglu
- Koç University Translational Medicine Research Center (KUTTAM) Rumeli Feneri, Sarıyer Istanbul Turkey
| | - Mika Sillanpää
- Environmental Engineering and Management Research Group Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Environment and Labour Safety Ton Duc Thang University Ho Chi Minh City Vietnam
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5
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Gupta N, Qayum A, Singh S, Mujwar S, Sangwan PL. Isolation, Cytotoxicity Evaluation, Docking, ADMET and Drug Likeness Studies of Secondary Metabolites from the Stem Bark of
Anthocephalus cadamba
(Roxb.). ChemistrySelect 2022. [DOI: 10.1002/slct.202202950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nidhi Gupta
- Natural Product and Medicinal Chemistry (NPMC) Division CSIR-Indian Institute of Integrative Medicine Jammu 180001 India
- Department of Pharmaceutical Chemistry M. M. College of Pharmacy Maharishi Markandeshwar (Deemed to be University) Mullana Ambala Haryana India 133207
| | - Arem Qayum
- Cancer Pharmacology Division CSIR-Indian Institute of Integrative Medicine Jammu 180001 India
| | - Shashank Singh
- Cancer Pharmacology Division CSIR-Indian Institute of Integrative Medicine Jammu 180001 India
| | - Somdutt Mujwar
- Chitkara College of Pharmacy Chitkara University, Rajpura Punjab India 140401
| | - Payare L. Sangwan
- Natural Product and Medicinal Chemistry (NPMC) Division CSIR-Indian Institute of Integrative Medicine Jammu 180001 India
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6
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Karami Fath M, Babakhaniyan K, Zokaei M, Yaghoubian A, Akbari S, Khorsandi M, Soofi A, Nabi-Afjadi M, Zalpoor H, Jalalifar F, Azargoonjahromi A, Payandeh Z, Alagheband Bahrami A. Anti-cancer peptide-based therapeutic strategies in solid tumors. Cell Mol Biol Lett 2022; 27:33. [PMID: 35397496 PMCID: PMC8994312 DOI: 10.1186/s11658-022-00332-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Nowadays, conventional medical treatments such as surgery, radiotherapy, and chemotherapy cannot cure all types of cancer. A promising approach to treat solid tumors is the use of tumor-targeting peptides to deliver drugs or active agents selectively. RESULT Introducing beneficial therapeutic approaches, such as therapeutic peptides and their varied methods of action against tumor cells, can aid researchers in the discovery of novel peptides for cancer treatment. The biomedical applications of therapeutic peptides are highly interesting. These peptides, owing to their high selectivity, specificity, small dimensions, high biocompatibility, and easy modification, provide good opportunities for targeted drug delivery. In recent years, peptides have shown considerable promise as therapeutics or targeting ligands in cancer research and nanotechnology. CONCLUSION This study reviews a variety of therapeutic peptides and targeting ligands in cancer therapy. Initially, three types of tumor-homing and cell-penetrating peptides (CPPs) are described, and then their applications in breast, glioma, colorectal, and melanoma cancer research are discussed.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Kimiya Babakhaniyan
- Department of Medical Surgical Nursing, School of Nursing and Midwifery, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Zokaei
- Department of Food Science and Technology, Faculty of Nutrition Science, Food Science and Technology/National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Veterinary Medicine, Beyza Branch, Islamic Azad University, Beyza, Iran
| | - Azadeh Yaghoubian
- Department of Exercise Physiology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sadaf Akbari
- Faculty of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdieh Khorsandi
- Department of Biotechnology, Faculty of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Asma Soofi
- Department of Physical Chemistry, School of Chemistry, College of Sciences, University of Tehran, Tehran, Iran
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of biological science, Tarbiat Modares University, Tehran, Iran
| | - Hamidreza Zalpoor
- American Association of Kidney Patients, Tampa, FL USA
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy & Autoimmunity (NIIMA), Universal Scientific Education & Research Network (USERN), Tehran, Iran
| | - Fateme Jalalifar
- School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | | | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden
| | - Armina Alagheband Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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7
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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8
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Gu Y, Iannuzzelli JA, Fasan R. MOrPH-PhD: A Phage Display System for the Functional Selection of Genetically Encoded Macrocyclic Peptides. Methods Mol Biol 2022; 2371:261-286. [PMID: 34596853 PMCID: PMC8493807 DOI: 10.1007/978-1-0716-1689-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for targeting biomolecules with high affinity and selectivity, making methods for the diversification and functional selection of these macrocycles highly valuable for drug discovery purposes. We recently reported a novel phage display platform (called MOrPH-PhD) for the creation and functional exploration of combinatorial libraries of genetically encoded cyclic peptides. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive non-canonical amino acid is integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. Using this system, it is possible to rapidly generate and screen large libraries of phage-displayed macrocyclic peptides (up to 108 to 1010 members) in order to identify high-affinity binders of a target protein of interest. Herein, we describe step-by-step protocols for the production of MOrPH-PhD libraries, the screening of these libraries against an immobilized protein target, and the isolation and characterization of functional macrocyclic peptides from these genetically encoded libraries.
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Affiliation(s)
- Yu Gu
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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9
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Peña-Guerrero J, Fernández-Rubio C, Burguete-Mikeo A, El-Dirany R, García-Sosa AT, Nguewa P. Discovery and Validation of Lmj_04_BRCT Domain, a Novel Therapeutic Target: Identification of Candidate Drugs for Leishmaniasis. Int J Mol Sci 2021; 22:ijms221910493. [PMID: 34638841 PMCID: PMC8508789 DOI: 10.3390/ijms221910493] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/13/2021] [Accepted: 09/23/2021] [Indexed: 01/09/2023] Open
Abstract
Since many of the currently available antileishmanial treatments exhibit toxicity, low effectiveness, and resistance, search and validation of new therapeutic targets allowing the development of innovative drugs have become a worldwide priority. This work presents a structure-based drug discovery strategy to validate the Lmj_04_BRCT domain as a novel therapeutic target in Leishmania spp. The structure of this domain was explored using homology modeling, virtual screening, and molecular dynamics studies. Candidate compounds were validated in vitro using promastigotes of Leishmania major, L. amazonensis, and L. infantum, as well as primary mouse macrophages infected with L. major. The novel inhibitor CPE2 emerged as the most active of a group of compounds against Leishmania, being able to significantly reduce the viability of promastigotes. CPE2 was also active against the intracellular forms of the parasites and significantly reduced parasite burden in murine macrophages without exhibiting toxicity in host cells. Furthermore, L. major promastigotes treated with CPE2 showed significant lower expression levels of several genes (α-tubulin, Cyclin CYCA, and Yip1) related to proliferation and treatment resistance. Our in silico and in vitro studies suggest that the Lmj_04_BRCT domain and its here disclosed inhibitors are new potential therapeutic options against leishmaniasis.
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Affiliation(s)
- José Peña-Guerrero
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, E-31008 Pamplona, Spain; (J.P.-G.); (C.F.-R.); (A.B.-M.); (R.E.-D.)
| | - Celia Fernández-Rubio
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, E-31008 Pamplona, Spain; (J.P.-G.); (C.F.-R.); (A.B.-M.); (R.E.-D.)
| | - Aroia Burguete-Mikeo
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, E-31008 Pamplona, Spain; (J.P.-G.); (C.F.-R.); (A.B.-M.); (R.E.-D.)
| | - Rima El-Dirany
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, E-31008 Pamplona, Spain; (J.P.-G.); (C.F.-R.); (A.B.-M.); (R.E.-D.)
| | - Alfonso T. García-Sosa
- Department of Molecular Technology, Institute of Chemistry, University of Tartu, 50411 Tartu, Estonia
- Correspondence: (A.T.G.-S.); (P.N.); Tel.: +372-737-5270 (A.T.G.-S.); +34-948-425-600 (ext. 6434) (P.N.)
| | - Paul Nguewa
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Instituto de Investigación Sanitaria de Navarra, Universidad de Navarra, E-31008 Pamplona, Spain; (J.P.-G.); (C.F.-R.); (A.B.-M.); (R.E.-D.)
- Correspondence: (A.T.G.-S.); (P.N.); Tel.: +372-737-5270 (A.T.G.-S.); +34-948-425-600 (ext. 6434) (P.N.)
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10
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Abd El-hafeez AA, Sun N, Chakraborty A, Ear J, Roy S, Chamarthi P, Rajapakse N, Das S, Luker KE, Hazra TK, Luker GD, Ghosh P. Regulation of DNA damage response by trimeric G-protein Signaling.. [DOI: 10.1101/2021.07.21.452842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractUpon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DNA damage hinges on the guanine nucleotide-exchange modulator of heterotrimeric G-protein, Giα•βγ, GIV/Girdin. GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1’s BRCT-modules via both phospho-dependent and -independent mechanisms. GIV promotes NHEJ, and binds and activates Gi and enhances the ‘free’ Gβγ→PI-3-kinase→Akt pathway, thus revealing the enigmatic origin of prosurvival Akt signals during dsDNA repair. Absence of GIV, or the loss of either of its two functions impaired DNA repair, and induced cell death when challenged with numerous cytotoxic agents. That GIV selectively binds few other BRCT-containing proteins suggests convergent signaling such that heterotrimeric G-proteins may finetune sensing, repair, and outcome after DNA damage.GRAPHIC ABSTRACTHIGHLIGHTSNon-receptor G protein modulator, GIV/Girdin binds BRCA1Binding occurs in both canonical and non-canonical modesGIV sequesters BRCA1 away from dsDNA breaks, suppresses HRActivation of Gi by GIV enhances Akt signals, favors NHEJIN BRIEFIn this work, the authors show that heterotrimeric G protein signaling that is triggered by non-receptor GEF, GIV/Girdin, in response to double-stranded DNA breaks is critical for decisive signaling events which favor non-homologous end-joining (NHEJ) and inhibit homologous recombination (HR).
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11
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Wang W, Khojasteh SC, Su D. Biosynthetic Strategies for Macrocyclic Peptides. Molecules 2021; 26:3338. [PMID: 34206124 PMCID: PMC8199541 DOI: 10.3390/molecules26113338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022] Open
Abstract
Macrocyclic peptides are predominantly peptide structures bearing one or more rings and spanning multiple amino acid residues. Macrocyclization has become a common approach for improving the pharmacological properties and bioactivity of peptides. A variety of ribosomal-derived and non-ribosomal synthesized cyclization approaches have been established. The biosynthesis of backbone macrocyclic peptides using seven new emerging methodologies will be discussed with regard to the features and strengths of each platform rather than medicinal chemistry tools. The mRNA display variant, known as the random nonstandard peptide integrated discovery (RaPID) platform, utilizes flexible in vitro translation (FIT) to access macrocyclic peptides containing nonproteinogenic amino acids (NAAs). As a new discovery approach, the ribosomally synthesized and post-translationally modified peptides (RiPPs) method involves the combination of ribosomal synthesis and the phage screening platform together with macrocyclization chemistries to generate libraries of macrocyclic peptides. Meanwhile, the split-intein circular ligation of peptides and proteins (SICLOPPS) approach relies on the in vivo production of macrocyclic peptides. In vitro and in vivo peptide library screening is discussed as an advanced strategy for cyclic peptide selection. Specifically, biosynthetic bicyclic peptides are highlighted as versatile and attractive modalities. Bicyclic peptides represent another type of promising therapeutics that allow for building blocks with a heterotrimeric conjugate to address intractable challenges and enable multimer complexes via linkers. Additionally, we discuss the cell-free chemoenzymatic synthesis of macrocyclic peptides with a non-ribosomal catalase known as the non-ribosomal synthetase (NRPS) and chemo-enzymatic approach, with recombinant thioesterase (TE) domains. Novel insights into the use of peptide library tools, activity-based two-hybrid screening, structure diversification, inclusion of NAAs, combinatorial libraries, expanding the toolbox for macrocyclic peptides, bicyclic peptides, chemoenzymatic strategies, and future perspectives are presented. This review highlights the broad spectrum of strategy classes, novel platforms, structure diversity, chemical space, and functionalities of macrocyclic peptides enabled by emerging biosynthetic platforms to achieve bioactivity and for therapeutic purposes.
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Affiliation(s)
| | | | - Dian Su
- Drug Metabolism and Disposition, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (W.W.); (S.C.K.)
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12
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Beheshtirouy S, Mirzaei F, Eyvazi S, Tarhriz V. Recent Advances in Therapeutic Peptides for Breast Cancer Treatment. Curr Protein Pept Sci 2021; 22:74-88. [PMID: 33208071 DOI: 10.2174/1389203721999201117123616] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/22/2020] [Accepted: 10/28/2020] [Indexed: 11/22/2022]
Abstract
Breast cancer is a heterogeneous malignancy and is the second leading cause of mortality among women around the world. Increasing the resistance to anti-cancer drugs in breast cancer cells persuades researchers to search the novel therapeutic approaches for the treatment of this malignancy. Among the novel methods, therapeutic peptides that target and disrupt tumor cells have been of great interest. Therapeutic peptides are short amino acid monomer chains with high specificity to bind and modulate a protein interaction of interest. Several advantages of peptides, such as specific binding on tumor cells surface, low molecular weight, and low toxicity on normal cells, make the peptides appealing therapeutic agents against solid tumors, particularly breast cancer. Also, the National Institutes of Health (NIH) describes therapeutic peptides as a suitable candidate for the treatment of drug-resistant breast cancer. In this review, we attempt to review the different therapeutic peptides against breast cancer cells that can be used in the treatment and diagnosis of the malignancy. Meanwhile, we presented an overview of peptide vaccines that have been developed for the treatment of breast cancer.
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Affiliation(s)
- Samad Beheshtirouy
- Department of Cardiothoracic Surgery, Imam Reza Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farhad Mirzaei
- Department of Neurosurgery, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Eyvazi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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13
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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14
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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15
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Unremitting progresses for phosphoprotein synthesis. Curr Opin Chem Biol 2020; 58:96-111. [PMID: 32889414 DOI: 10.1016/j.cbpa.2020.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 02/03/2023]
Abstract
Phosphorylation, one of the important protein post-translational modifications, is involved in many essential cellular processes. Site-specifical and homogeneous phosphoproteins can be used as probes for elucidating the protein phosphorylation network and as potential therapeutics for interfering their involved biological events. However, the generation of phosphoproteins has been challenging owing to the limitation of chemical synthesis and protein expression systems. Despite the pioneering discoveries in phosphoprotein synthesis, over the past decade, great progresses in this field have also been made to promote the biofunctional exploration of protein phosphorylation largely. Therefore, in this review, we mainly summarize recent advances in phosphoprotein synthesis, which includes five sections: 1) synthesis of the nonhydrolyzable phosphorylated amino acid mimetic building blocks, 2) chemical total and semisynthesis strategy, 3) in-cell and in vitro genetic code expansion strategy, 4) the late-stage modification strategy, 5) nonoxygen phosphoprotein synthesis.
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16
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Hacker DE, Abrigo NA, Hoinka J, Richardson SL, Przytycka TM, Hartman MCT. Direct, Competitive Comparison of Linear, Monocyclic, and Bicyclic Libraries Using mRNA Display. ACS COMBINATORIAL SCIENCE 2020; 22:306-310. [PMID: 32418423 PMCID: PMC7284801 DOI: 10.1021/acscombsci.0c00016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Peptide
macrocyclization is typically associated with the development of higher
affinity and more protease stable protein ligands, and, as such, is
an important tool in peptide drug discovery. Yet, within the context
of a diverse library, does cyclization give inherent advantages over
linear peptides? Here, we used mRNA display to create a peptide library
of diverse ring sizes and topologies (monocyclic, bicyclic, and
linear). Several rounds of in vitro selection against streptavidin
were performed and the winning peptide sequences were analyzed for
their binding affinities and overall topologies. The effect of adding
a protease challenge on the enrichment of various peptides was also
investigated. Taken together, the selection output yields insights
about the relative abundance of binders of various topologies within
a structurally diverse library.
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Affiliation(s)
- David E. Hacker
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, 23284, Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, 23219, Virginia, United States
| | - Nicolas A. Abrigo
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, 23284, Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, 23219, Virginia, United States
| | - Jan Hoinka
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, 20894, Maryland, United States
| | - Stacie L. Richardson
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, 23284, Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, 23219, Virginia, United States
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, 20894, Maryland, United States
| | - Matthew C. T. Hartman
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, 23284, Virginia, United States
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, 23219, Virginia, United States
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17
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Iannuzzelli JA, Fasan R. Expanded toolbox for directing the biosynthesis of macrocyclic peptides in bacterial cells. Chem Sci 2020; 11:6202-6208. [PMID: 32953014 PMCID: PMC7480269 DOI: 10.1039/d0sc01699c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
A new suite of unnatural amino acids is reported for directing the biosynthesis of genetically encoded macrocyclic peptides in live bacteria.
The macrocyclization of recombinant polypeptides by means of genetically encodable non-canonical amino acids has recently provided an attractive strategy for the screening and discovery of macrocyclic peptide inhibitors of protein–protein interactions. Here, we report the development of an expanded suite of electrophilic unnatural amino acids (eUAAs) useful for directing the biosynthesis of genetically encoded thioether-bridged macrocyclic peptides in bacterial cells (E. coli). These reagents are shown to provide efficient access to a broad range of macrocyclic peptide scaffolds spanning from 2 to 20 amino acid residues, with the different eUAAs offering complementary reactivity profiles toward mediating short- vs. long-range macrocyclizations. Swapping of the eUAA cyclization module in a cyclopeptide inhibitor of streptavidin and Keap1 led to compounds with markedly distinct binding affinity toward the respective target proteins, highlighting the effectiveness of this strategy toward tuning the structural and functional properties of bioactive macrocyclic peptides. The peptide cyclization strategies reported here expand opportunities for the combinatorial biosynthesis of natural product-like peptide macrocycles in bacterial cells or in combination with display platforms toward the discovery of selective agents capable of targeting proteins and protein-mediated interactions.
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Affiliation(s)
- Jacob A Iannuzzelli
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
| | - Rudi Fasan
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA .
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18
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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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19
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Frost JR, Essman JZ, Huang C, Pierson NA, Pissarnitski N, Meng T. Proline‐to‐cysteine
cyclization for generating conformationally constrained cyclic peptides. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John R. Frost
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Jake Z. Essman
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Chunhui Huang
- Discovery ChemistryMerck & Co., Inc Boston Massachusetts USA
| | | | - Natalya Pissarnitski
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
| | - Tao Meng
- Discovery Chemistry, Chemistry Capabilities for Accelerating TherapeuticsMerck & Co., Inc. Kenilworth New Jersey USA
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20
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Owens A, Iannuzzelli JA, Gu Y, Fasan R. MOrPH-PhD: An Integrated Phage Display Platform for the Discovery of Functional Genetically Encoded Peptide Macrocycles. ACS CENTRAL SCIENCE 2020; 6:368-381. [PMID: 32232137 PMCID: PMC7099587 DOI: 10.1021/acscentsci.9b00927] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 05/04/2023]
Abstract
Macrocyclic peptides represent attractive scaffolds for targeting protein-protein interactions, making methods for the diversification and functional selection of these molecules highly valuable for molecular discovery purposes. Here, we report the development of a novel strategy for the generation and high-throughput screening of combinatorial libraries of macrocyclic peptides constrained by a nonreducible thioether bridge. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive noncanonical amino acid was integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. This platform, named MOrPH-PhD, was successfully applied to produce and screen 105- to 108-member libraries of peptide macrocycles against three different protein targets, resulting in the discovery of a high-affinity binder for streptavidin (K D: 20 nM) and potent inhibitors of the therapeutically relevant proteins Kelch-like ECH-associated protein 1 (K D: 40 nM) and Sonic Hedgehog (K D: 550 nM). This work introduces and validates an efficient and general platform for the discovery and evolution of functional, conformationally constrained macrocyclic peptides useful for targeting proteins and protein-mediated interactions.
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21
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Liu W, Palovcak A, Li F, Zafar A, Yuan F, Zhang Y. Fanconi anemia pathway as a prospective target for cancer intervention. Cell Biosci 2020; 10:39. [PMID: 32190289 PMCID: PMC7075017 DOI: 10.1186/s13578-020-00401-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fanconi anemia (FA) is a recessive genetic disorder caused by biallelic mutations in at least one of 22 FA genes. Beyond its pathological presentation of bone marrow failure and congenital abnormalities, FA is associated with chromosomal abnormality and genomic instability, and thus represents a genetic vulnerability for cancer predisposition. The cancer relevance of the FA pathway is further established with the pervasive occurrence of FA gene alterations in somatic cancers and observations of FA pathway activation-associated chemotherapy resistance. In this article we describe the role of the FA pathway in canonical interstrand crosslink (ICL) repair and possible contributions of FA gene alterations to cancer development. We also discuss the perspectives and potential of targeting the FA pathway for cancer intervention.
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Affiliation(s)
- Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fang Li
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Alyan Zafar
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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22
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Newton MS, Cabezas-Perusse Y, Tong CL, Seelig B. In Vitro Selection of Peptides and Proteins-Advantages of mRNA Display. ACS Synth Biol 2020; 9:181-190. [PMID: 31891492 DOI: 10.1021/acssynbio.9b00419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
mRNA display is a robust in vitro selection technique that allows the selection of peptides and proteins with desired functions from libraries of trillions of variants. mRNA display relies upon a covalent linkage between a protein and its encoding mRNA molecule; the power of the technique stems from the stability of this link, and the large degree of control over experimental conditions afforded to the researcher. This article describes the major advantages that make mRNA display the method of choice among comparable in vivo and in vitro methods, including cell-surface display, phage display, and ribosomal display. We also describe innovative techniques that harness mRNA display for directed evolution, protein engineering, and drug discovery.
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Affiliation(s)
- Matilda S. Newton
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
- Department of Molecular, Cellular, and Developmental Biology & Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Yari Cabezas-Perusse
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Cher Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics & BioTechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
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23
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Kurdekar V, Giridharan S, Subbarao J, Nijaguna MB, Periasamy J, Boggaram S, Shivange AV, Sadasivam G, Padigaru M, Potluri V, Venkitaraman AR, Bharatham K. Structure-Guided Synthesis and Evaluation of Small-Molecule Inhibitors Targeting Protein-Protein Interactions of BRCA1 tBRCT Domain. ChemMedChem 2019; 14:1620-1632. [PMID: 31334915 DOI: 10.1002/cmdc.201900300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/20/2019] [Indexed: 01/09/2023]
Abstract
The tandem BRCT domains (tBRCT) of BRCA1 engage phosphoserine-containing motifs in target proteins to propagate intracellular signals initiated by DNA damage, thereby controlling cell cycle arrest and DNA repair. Recently, we identified Bractoppin, the first small-molecule inhibitor of the BRCA1 tBRCT domain, which selectively interrupts BRCA1-mediated cellular responses evoked by DNA damage. Here, we combine structure-guided chemical elaboration, protein mutagenesis and cellular assays to define the structural features responsible for Bractoppin's activity. Bractoppin fails to bind mutant forms of BRCA1 tBRCT bearing K1702A, a key residue mediating phosphopeptide recognition, or F1662R or L1701K that adjoin the pSer-recognition site. However, the M1775R mutation, which engages the Phe residue in the consensus phosphopeptide motif pSer-X-X-Phe, does not affect Bractoppin binding, confirming a binding mode distinct from the substrate phosphopeptide binding. We explored these structural features through structure-guided chemical elaboration and characterized structure-activity relationships (SARs) in biochemical assays. Two analogues, CCBT2088 and CCBT2103 were effective in abrogating BRCA1 foci formation and inhibiting G2 arrest induced by irradiation of cells. Collectively, our findings reveal structural features underlying the activity of a novel inhibitor of phosphopeptide recognition by the BRCA1 tBRCT domain, providing fresh insights to guide the development of inhibitors that target protein-protein interactions.
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Affiliation(s)
- Vadiraj Kurdekar
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Saranya Giridharan
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Jasti Subbarao
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Mamatha B Nijaguna
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Jayaprakash Periasamy
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Sanjana Boggaram
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Amol V Shivange
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Gayathri Sadasivam
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Muralidhara Padigaru
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Vijay Potluri
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
| | - Ashok R Venkitaraman
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India.,Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK
| | - Kavitha Bharatham
- Center for Chemical Biology & Therapeutics, InStem, Bellary Road, Bangalore, Karnataka, 560065, India
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24
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Iqbal ES, Richardson SL, Abrigo NA, Dods KK, Osorio Franco HE, Gerrish HS, Kotapati HK, Morgan IM, Masterson DS, Hartman MCT. A new strategy for the in vitro selection of stapled peptide inhibitors by mRNA display. Chem Commun (Camb) 2019; 55:8959-8962. [PMID: 31290487 DOI: 10.1039/c8cc10192b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydrocarbon stapled peptides are promising therapeutics for inhibition of intracellular protein-protein interactions. Here we develop a new high-throughput strategy for hydrocarbon stapled peptide discovery based on mRNA display of peptides containing α-methyl cysteine and cyclized with m-dibromoxylene. We focus on development of a peptide binder to the HPV16 E2 protein.
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Affiliation(s)
- Emil S Iqbal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - Stacie L Richardson
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - Nicolas A Abrigo
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - H Estheban Osorio Franco
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - Heather S Gerrish
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
| | - Hari Kiran Kotapati
- School of Mathematics & Natural Sciences, Chemistry & Biochemistry, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Iain M Morgan
- Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA and Philips Institute for Oral Health Research, Department of Oral and Craniofacial Molecular Biology, School of Dentistry, Virginia Commonwealth University, Box 980566, Richmond, VA 23298, USA
| | - Douglas S Masterson
- School of Mathematics & Natural Sciences, Chemistry & Biochemistry, 118 College Drive #5043, Hattiesburg, MS 39406, USA
| | - Matthew C T Hartman
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, P. O. Box 842006, Richmond, VA 23284, USA. and Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, VA 23298, USA
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25
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Passioura T, Liu W, Dunkelmann D, Higuchi T, Suga H. Display Selection of Exotic Macrocyclic Peptides Expressed under a Radically Reprogrammed 23 Amino Acid Genetic Code. J Am Chem Soc 2018; 140:11551-11555. [PMID: 30157372 DOI: 10.1021/jacs.8b03367] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bioactive naturally occurring macrocyclic peptides often exhibit a strong bias for hydrophobic residues. Recent advances in in vitro display technologies have made possible the identification of potent macrocyclic peptide ligands to protein targets of interest. However, such approaches have so far been restricted to using libraries composed of peptides containing mixtures of hydrophobic and hydrophilic/charged amino acids encoded by the standard genetic code. In the present study, we have demonstrated ribosomal expression of exotic macrocyclic peptides under a radically reprogrammed, relatively hydrophobic, genetic code, comprising 12 proteinogenic and 11 nonproteinogenic amino acids. Screening of this library for affinity to the interleukin-6 receptor (IL6R) as a case study successfully identified exotic macrocyclic peptide ligands with high affinity, validating the feasibility of this approach for the discovery of relatively hydrophobic exotic macrocyclic peptide ligands.
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Affiliation(s)
- Toby Passioura
- Department of Chemistry , Graduate School of Science, The University of Tokyo , 7-3-1, Hongo , Tokyo 113-0033 , Japan
| | - Wenyu Liu
- Department of Chemistry , Graduate School of Science, The University of Tokyo , 7-3-1, Hongo , Tokyo 113-0033 , Japan
| | - Daniel Dunkelmann
- Department of Chemistry , Graduate School of Science, The University of Tokyo , 7-3-1, Hongo , Tokyo 113-0033 , Japan
| | - Takashi Higuchi
- Department of Chemistry , Graduate School of Science, The University of Tokyo , 7-3-1, Hongo , Tokyo 113-0033 , Japan
| | - Hiroaki Suga
- Department of Chemistry , Graduate School of Science, The University of Tokyo , 7-3-1, Hongo , Tokyo 113-0033 , Japan
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26
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Richardson SL, Dods KK, Abrigo NA, Iqbal ES, Hartman MC. In vitro genetic code reprogramming and expansion to study protein function and discover macrocyclic peptide ligands. Curr Opin Chem Biol 2018; 46:172-179. [PMID: 30077877 DOI: 10.1016/j.cbpa.2018.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 01/26/2023]
Abstract
The ability to introduce non-canonical amino acids into peptides and proteins is facilitated by working within in vitro translation systems. Non-canonical amino acids can be introduced into these systems using sense codon reprogramming, stop codon suppression, and by breaking codon degeneracy. Here, we review how these techniques have been used to create proteins with novel properties and how they facilitate sophisticated studies of protein function. We also discuss how researchers are using in vitro translation experiments with non-canonical amino acids to explore the tolerance of the translation apparatus to artificial building blocks. Finally, we give several examples of how non-canonical amino acids can be combined with mRNA-displayed peptide libraries for the creation of protease-stable, macrocyclic peptide libraries for ligand discovery.
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Affiliation(s)
- Stacie L Richardson
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Kara K Dods
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Nicolas A Abrigo
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Emil S Iqbal
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA
| | - Matthew Ct Hartman
- Department of Chemistry, Virginia Commonwealth University (VCU), 1001 West Main Street, P.O. Box 842006, Richmond, USA; Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, USA.
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27
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Taylor RD, Rey-Carrizo M, Passioura T, Suga H. Identification of nonstandard macrocyclic peptide ligands through display screening. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:17-23. [PMID: 29249238 DOI: 10.1016/j.ddtec.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022]
Abstract
Techniques facilitating the synthesis and screening of very high diversity nonstandard macrocyclic peptide libraries have led to such compounds receiving increasing attention as potential drug candidates. Specifically, approaches which allow the use of non-proteinogenic amino acids are proving to be particularly effective, since they expand the accessible chemical space of the starting library and thus allow the identification of compounds with structural similarity to known drugs. This review focuses on mRNA display screening platforms for drug discovery and their combined use with genetic code reprogramming to identify novel macrocyclic peptides with high affinities for disease-related targets of interest.
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Affiliation(s)
- Rhys Dylan Taylor
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Matias Rey-Carrizo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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28
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Hacker DE, Hoinka J, Iqbal ES, Przytycka TM, Hartman MCT. Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display. ACS Chem Biol 2017; 12:795-804. [PMID: 28146347 DOI: 10.1021/acschembio.6b01006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitro selections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin). Both selections resulted in peptides with mid-nanomolar affinity, and the bicyclic selection yielded a peptide with remarkable protease resistance.
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Affiliation(s)
- David E. Hacker
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Jan Hoinka
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Emil S. Iqbal
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Teresa M. Przytycka
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Matthew C. T. Hartman
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
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29
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Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. PLoS Comput Biol 2016; 12:e1005057. [PMID: 27560145 PMCID: PMC4999267 DOI: 10.1371/journal.pcbi.1005057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/07/2016] [Indexed: 01/17/2023] Open
Abstract
Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design. Promiscuous proteins are commonly observed in biological systems, such as modular domains that recognize phosphopeptides during signal transduction. The use of phosphopeptides and compounds with phosphate groups as inhibitors to protein–protein interactions have attracted increasing interest for years. By using atomistic molecular dynamics simulations, we are able to perform detailed analyses of the dihedral space to explore protein fluctuation upon ligand binding to better understand promiscuous molecular recognition. Free energy calculation can further provide insights into the mechanism of binding, including both enthalpic and entropic contributions for molecular recognition, which assist in inhibitor design. Our calculation results show that pre-rigidifying a ligand is not always advantageous, suggesting the challenge in retaining optimized intermolecular interactions in pre-rigidified ligand. Instead, certain flexible ligands with multiple binding conformations can reduce entropic penalty, and therefore improves binding affinity. According to our computations, we can introduce new intermolecular interactions to flexible ligand to strengthen attractions while maintaining small entropic penalty by retaining its plasticity in the bound conformation. The study might cast light on a new general strategy for designing inhibitors targeting promiscuous modular domains and protein–protein interactions.
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30
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Schwochert J, Lao Y, Pye CR, Naylor MR, Desai PV, Gonzalez Valcarcel IC, Barrett JA, Sawada G, Blanco MJ, Lokey RS. Stereochemistry Balances Cell Permeability and Solubility in the Naturally Derived Phepropeptin Cyclic Peptides. ACS Med Chem Lett 2016; 7:757-61. [PMID: 27563399 DOI: 10.1021/acsmedchemlett.6b00100] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
Cyclic peptide (CP) natural products provide useful model systems for mapping "beyond-Rule-of-5" (bRo5) space. We identified the phepropeptins as natural product CPs with potential cell permeability. Synthesis of the phepropeptins and epimeric analogues revealed much more rapid cellular permeability for the natural stereochemical pattern. Despite being more cell permeable, the natural compounds exhibited similar aqueous solubility as the corresponding epimers, a phenomenon explained by solvent-dependent conformational flexibility among the natural compounds. When analyzing the polarity of the solution structures we found that neither the number of hydrogen bonds nor the total polar surface area accurately represents the solvation energies of the high and low dielectric conformations. This work adds to a growing number of natural CPs whose solvent-dependent conformational behavior allows for a balance between aqueous solubility and cell permeability, highlighting structural flexibility as an important consideration in the design of molecules in bRo5 chemical space.
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Affiliation(s)
- Joshua Schwochert
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Yongtong Lao
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Matthew R. Naylor
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Prashant V. Desai
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | | | - Jaclyn A. Barrett
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Geri Sawada
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - Maria-Jesus Blanco
- Lilly
Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States
| | - R. Scott Lokey
- Chemistry
and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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31
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Peraro L, Siegert TR, Kritzer JA. Conformational Restriction of Peptides Using Dithiol Bis-Alkylation. Methods Enzymol 2016; 580:303-32. [PMID: 27586339 DOI: 10.1016/bs.mie.2016.05.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Macrocyclic peptides are highly promising as inhibitors of protein-protein interactions. While many bond-forming reactions can be used to make cyclic peptides, most have limitations that make this chemical space challenging to access. Recently, a variety of cysteine alkylation reactions have been used in rational design and library approaches for cyclic peptide discovery and development. We and others have found that this chemistry is versatile and robust enough to produce a large variety of conformationally constrained cyclic peptides. In this chapter, we describe applications, methods, mechanistic insights, and troubleshooting for dithiol bis-alkylation reactions for the production of cyclic peptides. This method for efficient solution-phase macrocyclization is highly useful for the rapid production and screening of loop-based inhibitors of protein-protein interactions.
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Affiliation(s)
- L Peraro
- Tufts University, Medford, MA, United States
| | - T R Siegert
- Tufts University, Medford, MA, United States
| | - J A Kritzer
- Tufts University, Medford, MA, United States.
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32
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Kawakami T, Ogawa K, Hatta T, Goshima N, Natsume T. Directed Evolution of a Cyclized Peptoid-Peptide Chimera against a Cell-Free Expressed Protein and Proteomic Profiling of the Interacting Proteins to Create a Protein-Protein Interaction Inhibitor. ACS Chem Biol 2016; 11:1569-77. [PMID: 27010125 DOI: 10.1021/acschembio.5b01014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N-alkyl amino acids are useful building blocks for the in vitro display evolution of ribosomally synthesized peptides because they can increase the proteolytic stability and cell permeability of these peptides. However, the translation initiation substrate specificity of nonproteinogenic N-alkyl amino acids has not been investigated. In this study, we screened various N-alkyl amino acids and nonamino carboxylic acids for translation initiation with an Escherichia coli reconstituted cell-free translation system (PURE system) and identified those that efficiently initiated translation. Using seven of these efficiently initiating acids, we next performed in vitro display evolution of cyclized peptidomimetics against an arbitrarily chosen model human protein (β-catenin) cell-free expressed from its cloned cDNA (HUPEX) and identified a novel β-catenin-binding cyclized peptoid-peptide chimera. Furthermore, by a proteomic approach using direct nanoflow liquid chromatography-tandem mass spectrometry (DNLC-MS/MS), we successfully identified which protein-β-catenin interaction is inhibited by the chimera. The combination of in vitro display evolution of cyclized N-alkyl peptidomimetics and in vitro expression of human proteins would be a powerful approach for the high-speed discovery of diverse human protein-targeted cyclized N-alkyl peptidomimetics.
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Affiliation(s)
- Takashi Kawakami
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koji Ogawa
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohisa Hatta
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Naoki Goshima
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research
Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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