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Rossino G, Marchese E, Galli G, Verde F, Finizio M, Serra M, Linciano P, Collina S. Peptides as Therapeutic Agents: Challenges and Opportunities in the Green Transition Era. Molecules 2023; 28:7165. [PMID: 37894644 PMCID: PMC10609221 DOI: 10.3390/molecules28207165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides are at the cutting edge of contemporary research for new potent, selective, and safe therapeutical agents. Their rise has reshaped the pharmaceutical landscape, providing solutions to challenges that traditional small molecules often cannot address. A wide variety of natural and modified peptides have been obtained and studied, and many others are advancing in clinical trials, covering multiple therapeutic areas. As the demand for peptide-based therapies grows, so does the need for sustainable and environmentally friendly synthesis methods. Traditional peptide synthesis, while effective, often involves environmentally draining processes, generating significant waste and consuming vast resources. The integration of green chemistry offers sustainable alternatives, prioritizing eco-friendly processes, waste reduction, and energy conservation. This review delves into the transformative potential of applying green chemistry principles to peptide synthesis by discussing relevant examples of the application of such approaches to the production of active pharmaceutical ingredients (APIs) with a peptide structure and how these efforts are critical for an effective green transition era in the pharmaceutical field.
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Affiliation(s)
- Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Emanuela Marchese
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
- Department of Health Sciences, University “Magna Graecia”, Viale Europa, 88100 Catanzaro, Italy
| | - Giovanni Galli
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Francesca Verde
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Matteo Finizio
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
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2
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Chenna A, Khan WH, Dash R, Saraswat S, Chugh A, Rathore AS, Goel G. An efficient computational protocol for template-based design of peptides that inhibit interactions involving SARS-CoV-2 proteins. Proteins 2023; 91:1222-1234. [PMID: 37283297 DOI: 10.1002/prot.26511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/08/2023]
Abstract
The RNA-dependent RNA polymerase (RdRp) complex of SARS-CoV-2 lies at the core of its replication and transcription processes. The interfaces between holo-RdRp subunits are highly conserved, facilitating the design of inhibitors with high affinity for the interaction interface hotspots. We, therefore, take this as a model protein complex for the application of a structural bioinformatics protocol to design peptides that inhibit RdRp complexation by preferential binding at the interface of its core subunit nonstructural protein, nsp12, with accessory factor nsp7. Here, the interaction hotspots of the nsp7-nsp12 subunit of RdRp, determined from a long molecular dynamics trajectory, are used as a template. A large library of peptide sequences constructed from multiple hotspot motifs of nsp12 is screened in-silico to determine sequences with high geometric complementarity and interaction specificity for the binding interface of nsp7 (target) in the complex. Two lead designed peptides are extensively characterized using orthogonal bioanalytical methods to determine their suitability for inhibition of RdRp complexation. Binding affinity of these peptides to accessory factor nsp7, determined using a surface plasmon resonance (SPR) assay, is slightly better than that of nsp12: dissociation constant of 133nM and 167nM, respectively, compared to 473nM for nsp12. A competitive ELISA is used to quantify inhibition of nsp7-nsp12 complexation, with one of the lead peptides giving an IC50 of 25μM . Cell penetrability and cytotoxicity are characterized using a cargo delivery assay and MTT cytotoxicity assay, respectively. Overall, this work presents a proof-of-concept of an approach for rational discovery of peptide inhibitors of SARS-CoV-2 protein-protein interactions.
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Affiliation(s)
- Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Wajihul Hasan Khan
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
- Virology Unit, Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rozaleen Dash
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Chugh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, India
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3
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Patnaik SK, Ayyamperumal S, Jade D, Palathoti N, Akey KS, Jupudi S, Harrison MA, Ponnambalam S, Mj N, Mjn C. Virtual high throughput screening of natural peptides against ErbB1 and ErbB2 to identify potential inhibitors for cancer chemotherapy. J Biomol Struct Dyn 2023:1-24. [PMID: 37387589 DOI: 10.1080/07391102.2023.2226744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Human epidermal growth factor receptors (EGFR), namely ErbB1/HER1, ErbB2/HER2/neu, ErbB3/HER3, and ErbB4/HER4, the trans-membrane family of tyrosine kinase receptors, are overexpressed in many types of cancers. These receptors play an important role in cell proliferation, differentiation, invasion, metastasis and angiogenesis including unregulated activation of cancer cells. Overexpression of ErbB1 and ErbB2 that occurs in several types of cancers is associated with poor prognosis leading to resistance to ErbB1-directed therapies. In this connection, promising strategy to overcome the disadvantages of the existing chemotherapeutic drugs is the use of short peptides as anticancer agents. In the present study, we have performed virtual high throughput screening of natural peptides against ErbB1 and ErbB2 to identify potential dual inhibitors and identified five inhibitors based on their binding affinities, ADMET analysis, MD simulation studies and calculation of free energy of binding. These natural peptides could be further exploited for developing drugs for treating cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar Patnaik
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | - Selvaraj Ayyamperumal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | - Dhananjay Jade
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Nagarjuna Palathoti
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | - Krishna Swaroop Akey
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | | | | | - Nanjan Mj
- JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
| | - Chandrasekar Mjn
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamil Nadu, India
- School of Life Sciences, JSS Academy of Higher Education & Research(Ooty Campus), Ooty, Tamil Nadu, India
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4
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Shen F, Lin Y, Höhn M, Luo X, Döblinger M, Wagner E, Lächelt U. Iron-Gallic Acid Peptide Nanoparticles as a Versatile Platform for Cellular Delivery with Synergistic ROS Enhancement Effect. Pharmaceutics 2023; 15:1789. [PMID: 37513976 PMCID: PMC10385416 DOI: 10.3390/pharmaceutics15071789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Cytosolic delivery of peptides is of great interest owing to their biological functions, which could be utilized for therapeutic applications. However, their susceptibility to enzymatic degradation and multiple cellular barriers generally hinders their clinical application. Integration into nanoparticles, which can enhance the stability and membrane permeability of bioactive peptides, is a promising strategy to overcome extracellular and intracellular obstacles. Herein, we present a versatile platform for the cellular delivery of various cargo peptides by integration into metallo-peptidic coordination nanoparticles. Both termini of cargo peptides were conjugated with gallic acid (GA) to assemble GA-modified peptides into nanostructures upon coordination of Fe(III). Initial pre-complexation of Fe(III) by poly-(vinylpolypyrrolidon) (PVP) as a template favored the formation of nanoparticles, which are able to deliver the peptides into cells efficiently. Iron-gallic acid peptide nanoparticles (IGPNs) are stable in water and are supposed to generate reactive oxygen species (ROS) from endogenous H2O2 in cells via the Fenton reaction. The strategy was successfully applied to an exemplary set of peptide sequences varying in length (1-7 amino acids) and charge (negative, neutral, positive). To confirm the capability of transporting bioactive cargos into cells, pro-apoptotic peptides were integrated into IGPNs, which demonstrated potent killing of human cervix carcinoma HeLa and murine neuroblastoma N2a cells at a 10 µM peptide concentration via the complementary mechanisms of peptide-triggered apoptosis and Fe(III)-mediated ROS generation. This study demonstrates the establishment of IGPNs as a novel and versatile platform for the assembly of peptides into nanoparticles, which can be used for cellular delivery of bioactive peptides combined with intrinsic ROS generation.
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Affiliation(s)
- Faqian Shen
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Yi Lin
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Miriam Höhn
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Xianjin Luo
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | | | - Ernst Wagner
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
| | - Ulrich Lächelt
- Pharmaceutical Biotechnology, Department of Pharmacy, Center for NanoScience (CeNS), LMU Munich, 81377 Munich, Germany
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
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5
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Qiu R, Chen F, Álvarez Z, Clemons TD, Biswas S, Karver MR, Takata N, Sai H, Peng H, Weigand S, Palmer LC, Stupp SI. Supramolecular Nanofibers Block SARS-CoV-2 Entry into Human Host Cells. ACS Appl Mater Interfaces 2023; 15:26340-26348. [PMID: 37235485 DOI: 10.1021/acsami.3c02447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies on its spike protein binding to angiotensin-converting enzyme 2 (ACE2) on host cells to initiate cellular entry. Blocking the interactions between the spike protein and ACE2 offers promising therapeutic opportunities to prevent infection. We report here on peptide amphiphile supramolecular nanofibers that display a sequence from ACE2 in order to promote interactions with the SARS-CoV-2 spike receptor binding domain. We demonstrate that displaying this sequence on the surface of supramolecular assemblies preserves its α-helical conformation and blocks the entry of a pseudovirus and its two variants into human host cells. We also found that the chemical stability of the bioactive structures was enhanced in the supramolecular environment relative to the unassembled peptide molecules. These findings reveal unique advantages of supramolecular peptide therapies to prevent viral infections and more broadly for other targets as well.
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Affiliation(s)
- Ruomeng Qiu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Feng Chen
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Zaida Álvarez
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Medicine, Northwestern University, 676 N. St. Clair Street, Chicago, Illinois 60611, United States
| | - Tristan D Clemons
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Suvendu Biswas
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Mark R Karver
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Nozomu Takata
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Hiroaki Sai
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
| | - Han Peng
- Department of Dermatology, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Steven Weigand
- DuPont-Northwestern-Dow Collaborative Access Team (DND-CAT) Synchrotron Research Center, Advanced Photon Source (APS)/Argonne National Laboratory 432-A004, Northwestern University, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Liam C Palmer
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - Samuel I Stupp
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, 676 N. St. Clair Street, Chicago, Illinois 60611, United States
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Gattringer J, Gruber CW, Hellinger R. Peptide modulators of cell migration: Overview, applications and future development. Drug Discov Today 2023; 28:103554. [PMID: 36921670 DOI: 10.1016/j.drudis.2023.103554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Cell migration is a key physiological process in the development and homeostasis of multicellular organisms; errors in this complex system can trigger the development of cancer or inflammatory disorders. Therefore, modulating cell migration provides opportunities for drug discovery. Peptides are gaining importance on the global therapeutics market, given their unique properties compared with established small-molecule drugs or biologics. In this review, we identified over 470 peptides modulating cell migration and analyzed their characteristics. Over 95% of these peptides are in the discovery or preclinical stage, because the transition of peptide hits into a drug leads often results in a bottleneck in the development process. We summarize chemical strategies in (pre-)clinical development to enhance drug-like properties of bioactive peptides.
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Affiliation(s)
- Jasmin Gattringer
- Medical University of Vienna, Center for Physiology and Pharmacology, Schwarzspanierstrasse. 17, A-1090 Vienna, Austria
| | - Christian W Gruber
- Medical University of Vienna, Center for Physiology and Pharmacology, Schwarzspanierstrasse. 17, A-1090 Vienna, Austria
| | - Roland Hellinger
- Medical University of Vienna, Center for Physiology and Pharmacology, Schwarzspanierstrasse. 17, A-1090 Vienna, Austria.
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7
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Komar AA. Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics. Molecules 2023; 28:2383. [PMID: 36903628 PMCID: PMC10005171 DOI: 10.3390/molecules28052383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation.
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Affiliation(s)
- Anton A. Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; ; Tel.: +1-216-687-2516
- Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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8
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Khalily MP, Soydan M. Peptide-based diagnostic and therapeutic agents: Where we are and where we are heading? Chem Biol Drug Des 2023; 101:772-793. [PMID: 36366980 DOI: 10.1111/cbdd.14180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Peptides are increasingly present in all branches of medicine as innovative drugs, imaging agents, theragnostic, and constituent moieties of other sophisticated drugs such as peptide-drug conjugates. Due to new developments in chemical synthesis strategies, computational biology, recombinant technology, and chemical biology, peptide drug development has made a great progress in the last decade. Numerous natural peptides and peptide mimics have been obtained and studied, covering multiple therapeutic areas. Even though peptides have been investigated across the wide therapeutic spectrum, oncology, metabolism, and endocrinology are the most frequent medical indications of them. This review summarizes the current use of and the emerging new opportunities of peptides for diagnosis and treatment of various diseases.
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Affiliation(s)
- Melek P Khalily
- Department of Basic Science and Health, Cannabis Research Institute, Yozgat Bozok University, Yozgat, Turkey
| | - Medine Soydan
- Department of Chemistry, Faculty of Arts and Science, Middle East Technical University, Ankara, Turkey
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9
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Chen CH, Zan B, Ulmschneider JP, Wimley WC, Lu TK, Ulmschneider MB, Zhou L. Development of membrane-active peptide therapeutics in oncology. J Pept Sci 2023:e3482. [PMID: 36739581 DOI: 10.1002/psc.3482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/06/2023]
Abstract
Membrane-active peptides play an essential role in many living organisms and their immune systems and counter many infectious diseases. Many have dual or multiple mechanisms and can synergize with other molecules, like peptides, proteins, and small molecules. Although membrane-active peptides have been intensively studied in the past decades and more than 3500 sequences have been identified, only a few received approvals from the US Food and Drug Administration. In this review, we investigated all the peptide therapeutics that have entered the market or were subjected to preclinical and clinical studies to understand how they succeeded. With technological advancement (e.g., chemical modifications and pharmaceutical formulations) and a better understanding of the mechanism of action and the potential targets, we found at least five membrane-active peptide drugs that have entered preclinical/clinical phases and show promising results for cancer treatment. We summarized our findings in this review and provided insights into membrane-active anticancer peptide therapeutics.
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Affiliation(s)
- Charles H Chen
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Massachusetts, Boston, USA
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Jakob P Ulmschneider
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University, LA, New Orleans, USA
| | - Timothy K Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Liping Zhou
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Massachusetts, Boston, USA
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Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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11
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Mohammed GK, Böttger R, Krizsan A, Volke D, Mötzing M, Li SD, Knappe D, Hoffmann R. In Vitro Properties and Pharmacokinetics of Temporarily PEGylated Onc72 Prodrugs. Adv Healthc Mater 2023; 12:e2202368. [PMID: 36631971 DOI: 10.1002/adhm.202202368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/07/2023] [Indexed: 01/13/2023]
Abstract
The favorable properties of antimicrobial peptides (AMPs) to rapidly kill pathogens are often limited by unfavorable pharmacokinetics due to fast degradation and renal clearance rates. Here, a prodrug strategy linking proline-rich AMP Onc72 to polyethylene glycol (PEGs) with average molecular weights of 5 and 20 kDa via a peptide linker containing a protease cleavage site is tested for the first time in vivo. Onc72 is released from these 5k- and 20k-prodrugs in mouse serum with half-life times (t1/2 ) of 8 and 14 h, respectively. Importantly, PEGylation protects Onc72 from proteolytic degradation providing a prolonged release of Onc72, balancing the degradation of free Onc72, and leading to relatively stable Onc72 concentrations and high antibacterial activities. The prodrugs are not hemolytic on human erythrocytes and show only slight cytotoxic effects on human cell lines indicating promising safety margins. When administered subcutaneously to female CD-1 mice, the prodrugs elimination t1/2 are 66 min and ≈5.5 h, respectively, compared to 43 min of free Onc72. The maximal Onc72 plasma levels are obtained ≈1 and ≈8 h postadministration, respectively. In conclusion, the prodrugs provide extended elimination t1/2 and a constant release of Onc72 in mice, potentially limiting adverse effects and increasing efficacy.
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Affiliation(s)
- Gubran Khalil Mohammed
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany
| | - Roland Böttger
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Andor Krizsan
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany
| | - Marina Mötzing
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany
| | - Shyh-Dar Li
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Daniel Knappe
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany.,EnBiotix GmbH, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Leipzig University, 04103, Leipzig, Germany
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12
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Bose M, Farias Quipildor G, Ehrlich ME, Salton SR. Intranasal Peptide Therapeutics: A Promising Avenue for Overcoming the Challenges of Traditional CNS Drug Development. Cells 2022; 11:cells11223629. [PMID: 36429060 PMCID: PMC9688574 DOI: 10.3390/cells11223629] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022] Open
Abstract
The central nervous system (CNS) has, among all organ systems in the human body, the highest failure rate of traditional small-molecule drug development, ranging from 80-100% depending on the area of disease research. This has led to widespread abandonment by the pharmaceutical industry of research and development for CNS disorders, despite increased diagnoses of neurodegenerative disorders and the continued lack of adequate treatment options for brain injuries, stroke, neurodevelopmental disorders, and neuropsychiatric illness. However, new approaches, concurrent with the development of sophisticated bioinformatic and genomic tools, are being used to explore peptide-based therapeutics to manipulate endogenous pathways and targets, including "undruggable" intracellular protein-protein interactions (PPIs). The development of peptide-based therapeutics was previously rejected due to systemic off-target effects and poor bioavailability arising from traditional oral and systemic delivery methods. However, targeted nose-to-brain, or intranasal (IN), approaches have begun to emerge that allow CNS-specific delivery of therapeutics via the trigeminal and olfactory nerve pathways, laying the foundation for improved alternatives to systemic drug delivery. Here we review a dozen promising IN peptide therapeutics in preclinical and clinical development for neurodegenerative (Alzheimer's, Parkinson's), neuropsychiatric (depression, PTSD, schizophrenia), and neurodevelopmental disorders (autism), with insulin, NAP (davunetide), IGF-1, PACAP, NPY, oxytocin, and GLP-1 agonists prominent among them.
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Affiliation(s)
- Meenakshi Bose
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Farias Quipildor
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle E. Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen R. Salton
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Correspondence: ; Tel.: +1-212-824-9308
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13
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Abstract
Merck & Co. recently reported one of the first mRNA display-derived clinical candidates in a bioavailable inhibitor of proprotein convertase subtilisin/kexin type 9 (PCSK9). Herein, we discuss the chemical and pharmacological challenges surmounted in bringing this compound to trials and the current outlook for mRNA display-based therapeutic development.
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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
| | - 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, Chapel
Hill, North Carolina 27599, United States
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14
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Esposito S, Orsatti L, Pucci V. Subcutaneous Catabolism of Peptide Therapeutics: Bioanalytical Approaches and ADME Considerations. Xenobiotica 2022; 52:828-839. [PMID: 36039395 DOI: 10.1080/00498254.2022.2119180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Many peptide drugs such as insulin and glucagon-like peptide (GLP-1) analogues are successfully administered subcutaneously (SC). Following SC injection, peptides may undergo catabolism in the SC compartment before entering systemic circulation, which could compromise their bioavailability and in turn affect their efficacy.This review will discuss how both technology and strategy have evolved over the past years to further elucidate peptide SC catabolism.Modern bioanalytical technologies (particularly liquid chromatography-high-resolution mass spectrometry) and bioinformatics platforms for data mining has prompted the development of in silico, in vitro and in vivo tools for characterizing peptide SC catabolism to rapidly address proteolytic liabilities and, ultimately, guide the design of peptides with improved SC bioavailability.More predictive models able to recapitulate the interplay between SC catabolism and other factors driving SC absorption are highly desirable to improve in vitro/in vivo correlations.We envision the routine incorporation of in vitro and in vivo SC catabolism studies in ADME screening funnels to develop more effective peptide drugs for SC delivery.
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15
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Li M, Falk BT, Lu X, Schroder R, Mccoy M, Xu W, Yin DH, Gindy ME, D'Addio SM, Su Y. Molecular Mechanism of Antimicrobial Excipient-Induced Aggregation in Parenteral Formulations of Peptide Therapeutics. Mol Pharm 2022; 19:3267-3278. [PMID: 35917158 DOI: 10.1021/acs.molpharmaceut.2c00449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antimicrobial preservatives are used as functional excipients in multidose formulations of biological therapeutics to destroy or inhibit the growth of microbial contaminants, which may be introduced by repeatedly administering doses. Antimicrobial agents can also induce the biophysical instability of proteins and peptides, which presents a challenge in optimizing the drug product formulation. Elucidating the structural basis for aggregation aids in understanding the underlying mechanism and can offer valuable knowledge and rationale for designing drug substances and drug products; however, this remains largely unexplored due to the lack of high-resolution characterization. In this work, we utilize solution nuclear magnetic resonance (NMR) as an advanced biophysical tool to study an acylated 31-residue peptide, acyl-peptide A, and its interaction with commonly used antimicrobial agents, benzyl alcohol and m-cresol. Our results suggest that acyl-peptide A forms soluble octamers in the aqueous solution, which tumble slowly due to an increased molecular weight as measured by diffusion ordered spectroscopy and 1H relaxation measurement. The addition of benzyl alcohol does not induce aggregation of acyl-peptide A and has no chemical shift perturbation in 1H-1H NOESY spectra, suggesting no detectable interaction with the peptide. In contrast, the addition of 1% (w/v) m-cresol results in insoluble aggregates composed of 25% (w/w) peptides after a 24-hour incubation at room temperature as quantified by 1H NMR. Interestingly, 1H-13C heteronuclear single-quantum coherence and 1H-1H total correlation experiment spectroscopy have identified m-cresol and peptide interactions at specific residues, including Met, Lys, Glu, and Gln, suggesting that there may be a combination of hydrophobic, hydrogen bonding, and electrostatic interactions with m-cresol driving this phenomenon. These site-specific interactions have promoted the formation of higher-order oligomerization such as dimers and trimers of octamers, eventually resulting in insoluble aggregates. Our study has elucidated a structural basis of m-cresol-induced self-association that can inform the optimized design of drug substances and products. Moreover, it has demonstrated solution NMR as a high-resolution tool to investigate the structure and dynamics of biological drug products and provide an understanding of excipient-induced peptide and protein aggregation.
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Affiliation(s)
- Mingyue Li
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Bradley T Falk
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Xingyu Lu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ryan Schroder
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark Mccoy
- Computational and Structural Chemistry, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Wei Xu
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Daniel H Yin
- Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Marian E Gindy
- Small Molecule Science and Technology, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Suzanne M D'Addio
- Pharmaceutical Sciences, Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Yongchao Su
- Analytical Research & Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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16
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Mitchell W, Tamucci JD, Ng EL, Liu S, Birk AV, Szeto HH, May ER, Alexandrescu AT, Alder NN. Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds. eLife 2022; 11:75531. [PMID: 35913044 PMCID: PMC9342957 DOI: 10.7554/elife.75531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 07/03/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondria play a central role in metabolic homeostasis, and dysfunction of this organelle underpins the etiology of many heritable and aging-related diseases. Tetrapeptides with alternating cationic and aromatic residues such as SS-31 (elamipretide) show promise as therapeutic compounds for mitochondrial disorders. In this study, we conducted a quantitative structure-activity analysis of three alternative tetrapeptide analogs, benchmarked against SS-31, that differ with respect to aromatic side chain composition and sequence register. We present the first structural models for this class of compounds, obtained with Nuclear Magnetic Resonance (NMR) and molecular dynamics approaches, showing that all analogs except for SS-31 form compact reverse turn conformations in the membrane-bound state. All peptide analogs bound cardiolipin-containing membranes, yet they had significant differences in equilibrium binding behavior and membrane interactions. Notably, analogs had markedly different effects on membrane surface charge, supporting a mechanism in which modulation of membrane electrostatics is a key feature of their mechanism of action. The peptides had no strict requirement for side chain composition or sequence register to permeate cells and target mitochondria in mammalian cell culture assays. All four peptides were pharmacologically active in serum withdrawal cell stress models yet showed significant differences in their abilities to restore mitochondrial membrane potential, preserve ATP content, and promote cell survival. Within our peptide set, the analog containing tryptophan side chains, SPN10, had the strongest impact on most membrane properties and showed greatest efficacy in cell culture studies. Taken together, these results show that side chain composition and register influence the activity of these mitochondria-targeted peptides, helping provide a framework for the rational design of next-generation therapeutics with enhanced potency.
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Affiliation(s)
- Wayne Mitchell
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Jeffrey D Tamucci
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Emery L Ng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Shaoyi Liu
- Social Profit Network, Menlo Park, CA, United States
| | - Alexander V Birk
- Department of Biology, York College of CUNY, New York, NY, United States
| | - Hazel H Szeto
- Social Profit Network, Menlo Park, CA, United States
| | - Eric R May
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, United States
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17
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Buyanova M, Sahni A, Yang R, Sarkar A, Salim H, Pei D. Discovery of a Cyclic Cell-Penetrating Peptide with Improved Endosomal Escape and Cytosolic Delivery Efficiency. Mol Pharm 2022; 19:1378-1388. [PMID: 35405068 PMCID: PMC9175492 DOI: 10.1021/acs.molpharmaceut.1c00924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclic cell-penetrating peptide 12 (CPP12) is highly efficient for the cytosolic delivery of a variety of cargo molecules into mammalian cells in vitro and in vivo. However, its cytosolic entry efficiency is substantially reduced at lower concentrations or in the presence of serum proteins. In this study, CPP12 analogs were prepared by replacing its hydrophobic residues with amino acids of varying hydrophobicity and evaluated for cellular entry. Substitution of l-3-benzothienylalanine (Bta) for l-2-naphthylalanine (Nal) resulted in CPP12-2, which exhibits up to 3.8-fold higher cytosolic entry efficiency than CPP12, especially at low CPP concentrations; thanks to improved endosomal escape efficiency. CPP12-2 is well suited for the cytosolic delivery of highly potent cargos to achieve biological activity at low concentrations.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Rui Yang
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Amar Sarkar
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heba Salim
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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18
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Zhang P, Du C, Huang T, Hu S, Bai Y, Li C, Feng G, Gao Y, Li Z, Wang B, Hirvonen JT, Fan J, Santos HA, Liu D. Surface Adsorption-Mediated Ultrahigh Efficient Peptide Encapsulation with a Precise Ratiometric Control for Type 1 and 2 Diabetic Therapy. Small 2022; 18:e2200449. [PMID: 35229498 DOI: 10.1002/smll.202200449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Indexed: 06/14/2023]
Abstract
A surface adsorption strategy is developed to enable the engineering of microcomposites featured with ultrahigh loading capacity and precise ratiometric control of co-encapsulated peptides. In this strategy, peptide molecules (insulin, exenatide, and bivalirudin) are formulated into nanoparticles and their surface is decorated with carrier polymers. This polymer layer blocks the phase transfer of peptide nanoparticles from oil to water and, consequently, realizes ultrahigh peptide loading degree (up to 78.9%). After surface decoration, all three nanoparticles are expected to exhibit the properties of adsorbed polymer materials, which enables the co-encapsulation of insulin, exenatide, and bivalirudin with a precise ratiometric control. After solidification of this adsorbed polymer layer, the release of peptides is synchronously prolonged. With the help of encapsulation, insulin achieves 8 days of glycemic control in type 1 diabetic rats with one single injection. The co-delivery of insulin and exenatide (1:1) efficiently controls the glycemic level in type 2 diabetic rats for 8 days. Weekly administration of insulin and exenatide co-encapsulated microcomposite effectively reduces the weight gain and glycosylated hemoglobin level in type 2 diabetic rats. The surface adsorption strategy sets a new paradigm to improve the pharmacokinetic and pharmacological performance of peptides, especially for the combination of peptides.
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Affiliation(s)
- Pei Zhang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
| | - Chunyang Du
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Tianhe Huang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Shuai Hu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuancheng Bai
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Cong Li
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Guobing Feng
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Yue Gao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhi Li
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Baoxun Wang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
| | - Jouni T Hirvonen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
| | - Jin Fan
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hélder A Santos
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
- Department of Biomedical Engineering, W.J. Kolff Institute for Biomedical Engineering and Materials Science, University Medical Center Groningen/University of Groningen, Ant. Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Dongfei Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, 00014, Finland
- NMPA Key Laboratory for Research and Evaluation of Pharmaceutical Preparations and Excipients, China Pharmaceutical University, Nanjing, 210009, China
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19
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Gallo M, Defaus S, Andreu D. Disrupting GPCR Complexes with Smart Drug-like Peptides. Pharmaceutics 2022; 14:pharmaceutics14010161. [PMID: 35057055 PMCID: PMC8779866 DOI: 10.3390/pharmaceutics14010161] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a superfamily of proteins classically described as monomeric transmembrane (TM) receptors. However, increasing evidence indicates that many GPCRs form higher-order assemblies made up of monomers pertaining to identical (homo) or to various (hetero) receptors. The formation and structure of these oligomers, their physiological role and possible therapeutic applications raise a variety of issues that are currently being actively explored. In this context, synthetic peptides derived from TM domains stand out as powerful tools that can be predictably targeted to disrupt GPCR oligomers, especially at the interface level, eventually impairing their action. However, despite such potential, TM-derived, GPCR-disrupting peptides often suffer from inadequate pharmacokinetic properties, such as low bioavailability, a short half-life or rapid clearance, which put into question their therapeutic relevance and promise. In this review, we provide a comprehensive overview of GPCR complexes, with an emphasis on current studies using GPCR-disrupting peptides mimicking TM domains involved in multimerization, and we also highlight recent strategies used to achieve drug-like versions of such TM peptide candidates for therapeutic application.
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Affiliation(s)
| | - Sira Defaus
- Correspondence: (S.D.); (D.A.); Tel.: +34-933160868 (S.D. & D.A.)
| | - David Andreu
- Correspondence: (S.D.); (D.A.); Tel.: +34-933160868 (S.D. & D.A.)
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20
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Hirabayashi T, Shibato J, Kimura A, Yamashita M, Takenoya F, Shioda S. Potential Therapeutic Role of Pituitary Adenylate Cyclase-Activating Polypeptide for Dry Eye Disease. Int J Mol Sci 2022; 23:664. [PMID: 35054857 PMCID: PMC8775530 DOI: 10.3390/ijms23020664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/27/2022] Open
Abstract
Dry eye disease (DED) is caused by a reduction in the volume or quality of tears. The prevalence of DED is estimated to be 100 million in the developed world. As aging is a risk factor for DED, the prevalence of DED is expected to grow at a rapid pace in aging populations, thus creating an increased need for new therapies. This review summarizes DED medications currently in clinical use. Most current medications for DED focus on stimulating tear secretion, mucin secretion, or suppressing inflammation, rather than simply replenishing the ocular surface with moisture to improve symptoms. We recently reported that the neuropeptide PACAP (pituitary adenylate cyclase-activating polypeptide) induces tear secretion and suppresses corneal injury caused by a reduction in tears. Moreover, it has been reported that a PACAP in water and a 0.9% saline solution at +4 °C showed high stability and achieved 80-90% effectiveness after 2 weeks of treatment. These results reveal PACAP as a candidate DED medication. Further research on the clinical applications of PACAP in DED is necessary.
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Affiliation(s)
- Takahiro Hirabayashi
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama 244-0806, Japan
| | - Junko Shibato
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama 244-0806, Japan
| | - Ai Kimura
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama 244-0806, Japan
| | - Michio Yamashita
- Department of Physiology and Molecular Sciences, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Fumiko Takenoya
- Department of Physiology and Molecular Sciences, School of Pharmacy, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Seiji Shioda
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Shonan University of Medical Sciences, 16-48, Kamishinano, Totsuka-ku, Yokohama 244-0806, Japan
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21
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Massey O, Suphioglu C. Recent Advances in the Inhibition of the IL-4 Cytokine Pathway for the Treatment of Allergen-Induced Asthma. Int J Mol Sci 2021; 22:ijms222413655. [PMID: 34948449 PMCID: PMC8706302 DOI: 10.3390/ijms222413655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/23/2022] Open
Abstract
The IL-4 and IL-13 cytokine pathways play integral roles in stimulating IgE inflammation, with the IL-4 cytokine being a major cytokine in the etiology of thunderstorm asthma, atopic dermatitis, and allergic rhinitis. The increasing prevalence of thunderstorm asthma in the younger population and the lessening efficacy of corticosteroids and other anti-inflammatories has created a need for more effective pharmaceuticals. This review summarizes the IL-4 and IL-13 pathways while highlighting and discussing the current pathway inhibitors aimed at treating thunderstorm asthma and atopic dermatitis, as well as the potential efficacy of peptide therapeutics in this field.
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Affiliation(s)
- Oliver Massey
- NeuroAllergy Research Laboratory, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia;
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
| | - Cenk Suphioglu
- NeuroAllergy Research Laboratory, School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3216, Australia;
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC 3216, Australia
- Correspondence:
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22
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Grønning AGB, Kacprowski T, Schéele C. MultiPep: a hierarchical deep learning approach for multi-label classification of peptide bioactivities. Biol Methods Protoc 2021; 6:bpab021. [PMID: 34909478 PMCID: PMC8665375 DOI: 10.1093/biomethods/bpab021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/28/2021] [Accepted: 11/17/2021] [Indexed: 11/14/2022] Open
Abstract
Peptide-based therapeutics are here to stay and will prosper in the future. A key step in identifying novel peptide-drugs is the determination of their bioactivities. Recent advances in peptidomics screening approaches hold promise as a strategy for identifying novel drug targets. However, these screenings typically generate an immense number of peptides and tools for ranking these peptides prior to planning functional studies are warranted. Whereas a couple of tools in the literature predict multiple classes, these are constructed using multiple binary classifiers. We here aimed to use an innovative deep learning approach to generate an improved peptide bioactivity classifier with capacity of distinguishing between multiple classes. We present MultiPep: a deep learning multi-label classifier that assigns peptides to zero or more of 20 bioactivity classes. We train and test MultiPep on data from several publically available databases. The same data are used for a hierarchical clustering, whose dendrogram shapes the architecture of MultiPep. We test a new loss function that combines a customized version of Matthews correlation coefficient with binary cross entropy (BCE), and show that this is better than using class-weighted BCE as loss function. Further, we show that MultiPep surpasses state-of-the-art peptide bioactivity classifiers and that it predicts known and novel bioactivities of FDA-approved therapeutic peptides. In conclusion, we present innovative machine learning techniques used to produce a peptide prediction tool to aid peptide-based therapy development and hypothesis generation.
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Affiliation(s)
- Alexander G B Grønning
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, 38106 Braunschweig, Germany.,Braunschweig Integrated Centre for Systems Biology (BRICS), 38106 Braunschweig, Germany
| | - Camilla Schéele
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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23
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Mannes M, Martin C, Menet C, Ballet S. Wandering beyond small molecules: peptides as allosteric protein modulators. Trends Pharmacol Sci 2021; 43:406-423. [PMID: 34857409 DOI: 10.1016/j.tips.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/28/2022]
Abstract
Recent years have seen the rise of allosteric modulation as an innovative approach for drug design and discovery, efforts which culminated in the development of several clinical candidates. Allosteric modulation of many drug targets, including mainly membrane-embedded receptors, have been vastly explored through small molecule screening campaigns, but much less attention has been paid to peptide-based allosteric modulators. However, peptides have a significant impact on the pharmaceutical industry due to the typically higher potency and selectivity for their targets, as compared with small molecule therapeutics. Therefore, peptides represent one of the most promising classes of molecules that can modulate key biological pathways. Here, we report on the allosteric modulation of proteins (ranging from G protein-coupled receptors to specific protein-protein interactions) by peptides for applications in drug discovery.
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Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
| | - Christel Menet
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 30, Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.
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24
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Oliveira CS, Torres MDT, Pedron CN, Andrade VB, Silva PI, Silva FD, de la Fuente-Nunez C, Oliveira VX. Synthetic Peptide Derived from Scorpion Venom Displays Minimal Toxicity and Anti-infective Activity in an Animal Model. ACS Infect Dis 2021; 7:2736-2745. [PMID: 34463484 DOI: 10.1021/acsinfecdis.1c00261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multidrug-resistant bacteria represent a global health problem increasingly leading to infections that are untreatable with our existing antibiotic arsenal. Therefore, it is critical to identify novel effective antimicrobials. Venoms represent an underexplored source of potential antibiotic molecules. Here, we engineered a peptide (IsCT1-NH2) derived from the venom of the scorpion Opisthacanthus madagascariensis, whose application as an antimicrobial had been traditionally hindered by its high toxicity. Through peptide design and the knowledge obtained in preliminary studies with single and double-substituted analogs, we engineered IsCT1 derivatives with multiple amino acid substitutions to assess the impact of net charge on antimicrobial activity and toxicity. We demonstrate that increased net charge (from +3 to +6) significantly reduced toxicity toward human erythrocytes. Our lead synthetic peptide, [A]1[K]3[F]5[K]8-IsCT1-NH2 (net charge of +4), exhibited increased antimicrobial activity against Gram-negative and Gram-positive bacteria in vitro and enhanced anti-infective activity in a mouse model. Mechanism of action studies revealed that the increased antimicrobial activity of our lead molecule was due, at least in part, to its enhanced ability to permeabilize the outer membrane and depolarize the cytoplasmic membrane. In summary, we describe a simple method based on net charge tuning to turn highly toxic venom-derived peptides into viable therapeutics.
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Affiliation(s)
- Cyntia Silva Oliveira
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cibele Nicolaski Pedron
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
| | - Viviane Brito Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
| | - Pedro Ismael Silva
- Instituto Butantan, Laboratório Especial de Toxinologia Aplicada, São Paulo, SP 05503900, Brazil
| | - Fernanda Dias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Vani Xavier Oliveira
- Escola Paulista de Medicina, Programa de pós-graduação em Biologia Molecular, Universidade Federal de São Paulo, São Paulo, SP 04044020, Brazil
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210580, Brazil
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25
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Panchal D, Kataria J, Patel K, Crowe K, Pai V, Azizogli AR, Kadian N, Sanyal S, Roy A, Dodd-O J, Acevedo-Jake AM, Kumar VA. Peptide-Based Inhibitors for SARS-CoV-2 and SARS-CoV. Adv Ther (Weinh) 2021; 4:2100104. [PMID: 34514085 PMCID: PMC8420164 DOI: 10.1002/adtp.202100104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/14/2021] [Indexed: 12/20/2022]
Abstract
The COVID‐19 (coronavirus disease) global pandemic, caused by the spread of the SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus 2) virus, currently has limited treatment options which include vaccines, anti‐virals, and repurposed therapeutics. With their high specificity, tunability, and biocompatibility, small molecules like peptides are positioned to act as key players in combating SARS‐CoV‐2, and can be readily modified to match viral mutation rate. A recent expansion of the understanding of the viral structure and entry mechanisms has led to the proliferation of therapeutic viral entry inhibitors. In this comprehensive review, inhibitors of SARS and SARS‐CoV‐2 are investigated and discussed based on therapeutic design, inhibitory mechanistic approaches, and common targets. Peptide therapeutics are highlighted, which have demonstrated in vitro or in vivo efficacy, discuss advantages of peptide therapeutics, and common strategies in identifying targets for viral inhibition.
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Affiliation(s)
- Disha Panchal
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Jeena Kataria
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Kamiya Patel
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Kaytlyn Crowe
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Varun Pai
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Abdul-Rahman Azizogli
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Neil Kadian
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Sreya Sanyal
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Abhishek Roy
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Joseph Dodd-O
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Amanda M Acevedo-Jake
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
| | - Vivek A Kumar
- Department of Biomedical Engineering New Jersey Institute of Technology Newark NJ 07102 USA.,Department of Biomedical Engineering Department of Chemical Biological and Pharmaceutical Engineering New Jersey Institute of Technology Newark NJ 07102 USA
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26
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Abstract
Peptide aptamers are short amino acid chains that are capable of binding specifically to ligands in the same way as their much larger counterparts, antibodies. Ligands of therapeutic interest that can be targeted are other peptide chains or loops located on the surface of protein receptors (e.g., GCPR), which take part in cell-to-cell communications either directly or via the intermediary of hormones or signalling molecules. To confer on aptamers the same sort of conformational rigidity that characterises an antibody binding site, aptamers are often constructed in the form of cyclic peptides, on the assumption that this will encourage stronger binding interactions than would occur if the aptamers were simply linear chains. However, no formal studies have been conducted to confirm the hypothesis that linear peptides will engage in stronger binding interactions with cyclic peptides than with other linear peptides. In this study, the interaction of a model cyclic decamer with a series of linear peptide constructs was compared with that of a linear peptide with the same sequence, showing that the cyclic configuration does confer benefits by increasing the strength of binding.
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Affiliation(s)
- Roger R. C. New
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, Hendon, London NW4 4BT, UK
- Correspondence: or
| | - Tam T. T. Bui
- Centre for Biomolecular Spectroscopy and Institute of Pharmaceutical Science, King’s College, London SE1 1UL, UK;
| | - Michal Bogus
- Vaxcine (UK) Limited, London Bioscience Innovation Centre, London NW1 0NH, UK;
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27
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Salekeen R, Ahmed A, Islam ME, Billah MM, Rahman H, Islam KMD. In-silico screening of bioactive phytopeptides for novel anti-ageing therapeutics. J Biomol Struct Dyn 2020; 40:4475-4487. [PMID: 33317397 DOI: 10.1080/07391102.2020.1859411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
A metabolic network of energy-sensing molecular pathways drives the biological ageing process. Regulating certain network elements can help decelerate the ageing process and ameliorate ageing associated disorders. Bioactive phytopeptides are a prospective avenue for anti-ageing therapeutics and rejuvenation biotechnology. The present study investigates the potential of therapeutic plant peptides against cellular senescence by targeting three key proteins in the ageing network - target of rapamycin (mTOR), adenosine monophosphate-activated protein kinase (AMPK) and sirtuin 1 (SIRT1). This investigation screened a library of reported bioactive peptides using standard cheminformatic methods including in-silico ADMET, molecular docking, molecular dynamics simulation and molecular mechanics calculation. The retrieved simulation data predict 25 diverse phytopeptides as potential safe and drug-like anti-ageing biologics with half-lives >20 h and bioavailability scores >0.40. The best docked peptide, Cycloleonuripeptide B, exhibited strong binding affinity and stable complex formation with mTOR (-17.5 kCal/mol), SIRT1 (-28.54 kCal/mol) and two active sites in AMPK (-41.8 kCal/mol; -36.0 kCal/mol) during molecular dynamics simulations. The computational study acts as a foundation for future laboratory and clinical research into the potential of repurposing therapeutic phytopeptides against cellular senescence and associated pathophysiology. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Asif Ahmed
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Emdadul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Hafizur Rahman
- Department of Environmental Science and Management School of Environment and Life Sciences, Independent University Bangladesh, Dhaka, Bangladesh
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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28
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Dougherty PG, Karpurapu M, Koley A, Lukowski JK, Qian Z, Nirujogi TS, Rusu L, Chung S, Hummon AB, Li HW, Christman JW, Pei D. A Peptidyl Inhibitor that Blocks Calcineurin-NFAT Interaction and Prevents Acute Lung Injury. J Med Chem 2020; 63:12853-12872. [PMID: 33073986 PMCID: PMC8011862 DOI: 10.1021/acs.jmedchem.0c01236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is an inflammatory lung disease with a high morbidity and mortality rate, for which no pharmacologic treatment is currently available. Our previous studies discovered that a pivotal step in the disease process is the activation of the nuclear factor of activated T cells (NFAT) c3 in lung macrophages, suggesting that inhibitors against the upstream protein phosphatase calcineurin should be effective for prevention/treatment of ARDS. Herein, we report the development of a highly potent, cell-permeable, and metabolically stable peptidyl inhibitor, CNI103, which selectively blocks the interaction between calcineurin and NFATc3, through computational and medicinal chemistry. CNI103 specifically inhibited calcineurin signaling in vitro and in vivo and exhibited a favorable pharmacokinetic profile, broad tissue distribution following different routes of administration, and minimal toxicity. Our data indicate that CNI103 is a promising novel treatment for ARDS and other inflammatory diseases.
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Affiliation(s)
- Patrick G. Dougherty
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Manjula Karpurapu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
| | - Jessica K. Lukowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Entrada Therapeutics, 50 Northern Avenue, Boston, MA 02210, United States
| | - Teja Srinivas Nirujogi
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
- East Liverpool City Hospital, 425 W 5th Street, East Liverpool, Ohio 43920, United States
| | - Luiza Rusu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Sangwoon Chung
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
- Comprehensive Cancer Center, The Ohio State University, Columbus OH, 43210, United States
| | - Hao W. Li
- Columbia Center for Translational Immunology, Columbia University, 650 W. 168 Street, New York, New York 10032, United States
| | - John W. Christman
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12 Ave., Columbus, OH 43210, United States
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29
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Abstract
INTRODUCTION In this review, recent developments and applications with cell-penetrating peptides (CPP) are discussed. CPPs are widely used tools for the delivery of various macromolecular therapeutics, such as proteins and nucleic acids. AREAS COVERED The current review focuses on recent important advances and reports that demonstrate high clinical and translational potential. Most important clinical developments have occurred with the CPP-drug conjugate approaches that target various protein-protein interactions, and these have been highlighted subsequently. Most of the applications are targeting cancer, but recently, noteworthy advances have taken place in the field of antisense oligonucleotides and muscular dystrophies, lung targeting, and trans-BBB targeting. EXPERT OPINION Successful applications and clinical development with the drug conjugate approaches are discussed. On the other hand, the reasons of why the nanoparticle approaches are not as far in development are analyzed.
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Affiliation(s)
- Kaido Kurrikoff
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Birgit Vunk
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Ülo Langel
- University of Tartu, Institute of Technology, Tartu, Estonia.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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30
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Agrawal P, Bhagat D, Mahalwal M, Sharma N, Raghava GPS. AntiCP 2.0: an updated model for predicting anticancer peptides. Brief Bioinform 2020; 22:5881378. [PMID: 32770192 DOI: 10.1093/bib/bbaa153] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/01/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Increasing use of therapeutic peptides for treating cancer has received considerable attention of the scientific community in the recent years. The present study describes the in silico model developed for predicting and designing anticancer peptides (ACPs). ACPs residue composition analysis show the preference of A, F, K, L and W. Positional preference analysis revealed that residues A, F and K are favored at N-terminus and residues L and K are preferred at C-terminus. Motif analysis revealed the presence of motifs like LAKLA, AKLAK, FAKL and LAKL in ACPs. Machine learning models were developed using various input features and implementing different machine learning classifiers on two datasets main and alternate dataset. In the case of main dataset, dipeptide composition based ETree classifier model achieved maximum Matthews correlation coefficient (MCC) of 0.51 and 0.83 area under receiver operating characteristics (AUROC) on the training dataset. In the case of alternate dataset, amino acid composition based ETree classifier performed best and achieved the highest MCC of 0.80 and AUROC of 0.97 on the training dataset. Five-fold cross-validation technique was implemented for model training and testing, and their performance was also evaluated on the validation dataset. Best models were implemented in the webserver AntiCP 2.0, which is freely available at https://webs.iiitd.edu.in/raghava/anticp2/. The webserver is compatible with multiple screens such as iPhone, iPad, laptop and android phones. The standalone version of the software is available at GitHub; docker-based container also developed.
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Affiliation(s)
- Piyush Agrawal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Dhruv Bhagat
- Indraprastha Institute of Information Technology, New Delhi, India
| | - Manish Mahalwal
- Indraprastha Institute of Information Technology, New Delhi, India
| | - Neelam Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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31
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Yan J, Ji F, Yan S, You W, Ma F, Li F, Huang Y, Liu W, He W. A general-purpose Nanohybrid fabricated by Polymeric Au(I)-peptide precursor to wake the function of Peptide Therapeutics. Theranostics 2020; 10:8513-8527. [PMID: 32754260 PMCID: PMC7392018 DOI: 10.7150/thno.47243] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/28/2020] [Indexed: 01/10/2023] Open
Abstract
Peptide-derived nanocomposites have been exhibiting fascinating biological advantages, including but not limited to excellent biocompatibility, biological degradation, high targetability and subsequent potent therapeutic efficacy. While some successes have been achieved in the nanoengineering of peptide-based architectures with defined dimensions and medical functions, enormous challenges remain about clinical nano-pharmaceutics of peptides, especially those modulating intracellular protein-protein interactions (PPIs). Methods: We developed a general method to translate intracellular-PPI-targeted peptides into a bioavailable peptide-auric spheroidal nanohybrid (SNH), for which polymeric peptide-Auric precursors [Au1+-S-peptide]n are in-situ reduced on the surface of gold nanoseeds via a simple and mild reaction. As proofs of concept, three cytomembrane-impenetrable peptides with different physicochemical properties were successfully engineered into stable and tumor-specific SNH respectively. Results: To highlight the advantage of SNH, PMI, a hydrophobic and enzyme-intolerant peptide capable of p53 restoration, was selected to challenge the power of SNH in a colon tumor xenografts model. PMI-Au SNH in vivo suppressed tumor growth potently after three administrations: intravenous injection, intraperitoneal injection and gastric perfusion, and maintained a favorable therapeutic safety. Conclusion: This therapeutically feasible strategy of peptide nanoengineering will allow us to fabricate a series of nanomedicines to modulate carcinogenic PPIs that hide and multiply inside cells, and in all likelihood reinvigorate the development of peptide drug against wide varieties of human diseases.
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Affiliation(s)
- Jin Yan
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Department of Tumor and Immunology in precision medical institute, Western China Science and Technology Innovation Port, Xi'an, 710004, PR. China
| | - Fanpu Ji
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Department of Infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education of China, Xi'an, China
| | - Siqi Yan
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
| | - Weiming You
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Department of Tumor and Immunology in precision medical institute, Western China Science and Technology Innovation Port, Xi'an, 710004, PR. China
| | - Fang Ma
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Department of Tumor and Immunology in precision medical institute, Western China Science and Technology Innovation Port, Xi'an, 710004, PR. China
| | - Fanni Li
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
| | - Yinong Huang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, Shaanxi 710003, PR. China
| | - Wenjia Liu
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
- Department of Tumor and Immunology in precision medical institute, Western China Science and Technology Innovation Port, Xi'an, 710004, PR. China
| | - Wangxiao He
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, PR. China
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, PR. China
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32
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Chilewski SD, Bhosale D, Dees S, Hutchinson I, Trimble R, Pontiggia L, Mercier I, Jasmin JF. Development of CAPER peptides for the treatment of triple negative breast cancer. Cell Cycle 2020; 19:432-447. [PMID: 31931653 PMCID: PMC7100886 DOI: 10.1080/15384101.2020.1711579] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/06/2019] [Accepted: 12/16/2019] [Indexed: 10/26/2022] Open
Abstract
Triple negative breast cancer (TNBC) is a heterogeneous disease, which lacks expression of the estrogen receptor (ER), progesterone receptor (PR) and the human epidermal growth factor 2 receptor (HER2). This subtype of breast cancer has the poorest prognosis with limited therapies currently available, and hence additional options are needed. CAPER is a coactivator of the activator protein-1 (AP-1) (interacting specifically with the c-Jun component) and the ER and is known to be involved in human breast cancer pathogenesis. Recent published data have demonstrated a role for CAPER in TNBC and, as such, disrupting the function of CAPER with c-Jun could be a novel approach to treat TNBC patients. The data presented here shows the development and in vitro testing of CAPER-derived peptides that inhibit the coactivator activity of CAPER with c-Jun. These CAPER peptides result in a decrease in cell number and an increase in apoptosis in two TNBC cell lines, MDA-MB-231 and BT-549, while having no effect on the non-tumorigenic cell line MCF 10A. Additionally, two modes of action were demonstrated which appear to be cell line dependent: 1) a modulation of phosphorylated c-Jun leading to a decrease in Bcl-2 in MDA-MB-231 cells and a decrease in p21 in BT-549 cells and 2) a decrease in DNA repair proteins, leading to impaired DNA repair function in MDA-MB-231 cells. The data presented here supports further development of CAPER-derived peptides for the treatment of TNBC.
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Affiliation(s)
- Shannon D. Chilewski
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Devyani Bhosale
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Sundee Dees
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Isaac Hutchinson
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Rachel Trimble
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Laura Pontiggia
- Department of Mathematics, Physics and Statistics, Misher College of Arts and Sciences, University of the Sciences, Philadelphia, PA, USA
| | - Isabelle Mercier
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
| | - Jean-Francois Jasmin
- Department of Pharmaceutical Sciences, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USA
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33
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Chen CH, Lu TK. Development and Challenges of Antimicrobial Peptides for Therapeutic Applications. Antibiotics (Basel) 2020; 9:antibiotics9010024. [PMID: 31941022 PMCID: PMC7168295 DOI: 10.3390/antibiotics9010024] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 12/27/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022] Open
Abstract
More than 3000 antimicrobial peptides (AMPs) have been discovered, seven of which have been approved by the U.S. Food and Drug Administration (FDA). Now commercialized, these seven peptides have mostly been utilized for topical medications, though some have been injected into the body to treat severe bacterial infections. To understand the translational potential for AMPs, we analyzed FDA-approved drugs in the FDA drug database. We examined their physicochemical properties, secondary structures, and mechanisms of action, and compared them with the peptides in the AMP database. All FDA-approved AMPs were discovered in Gram-positive soil bacteria, and 98% of known AMPs also come from natural sources (skin secretions of frogs and toxins from different species). However, AMPs can have undesirable properties as drugs, including instability and toxicity. Thus, the design and construction of effective AMPs require an understanding of the mechanisms of known peptides and their effects on the human body. This review provides an overview to guide the development of AMPs that can potentially be used as antimicrobial drugs.
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Affiliation(s)
- Charles H. Chen
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Correspondence: (C.H.C.); (T.K.L.)
| | - Timothy K. Lu
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA
- Correspondence: (C.H.C.); (T.K.L.)
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Kurcinski M, Badaczewska‐Dawid A, Kolinski M, Kolinski A, Kmiecik S. Flexible docking of peptides to proteins using CABS-dock. Protein Sci 2020; 29:211-222. [PMID: 31682301 PMCID: PMC6933849 DOI: 10.1002/pro.3771] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/12/2022]
Abstract
Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein-peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead.
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Affiliation(s)
- Mateusz Kurcinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | | | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research CentrePolish Academy of SciencesWarsawPoland
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research CenterUniversity of WarsawWarsawPoland
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35
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Chittepu VCSR, Kalhotra P, Osorio-Gallardo T, Jiménez-Martínez C, Torre RRRDL, Gallardo-Velazquez T, Osorio-Revilla G. New Molecular Insights into the Inhibition of Dipeptidyl Peptidase-4 by Natural Cyclic Peptide Oxytocin. Molecules 2019; 24:E3887. [PMID: 31661941 PMCID: PMC6864445 DOI: 10.3390/molecules24213887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 11/21/2022] Open
Abstract
Protease inhibition has led to treating many diseases and has been successful in producing many commercial drugs by pharmaceutical companies. Among many proteases, serine protease has been attractive in treating metabolic disorder diabetes mellitus (DM). Gliptins have been proven to inhibit dipeptidyl peptidase-4 (DPP4), a serine protease, and are an emerging therapeutic drug target to reduce blood glucose levels, but until now there is no natural cyclic peptide proven to inhibit serine protease DPP4. This study demonstrates the potential mechanism of natural cyclic peptide oxytocin (OXT) as a DPP4 inhibitor. To achieve this, initially, activity atlas and field-based models of DPP4 inhibitors were utilized to predict the possible features of positive and negative electrostatic, hydrophobic, and activity shapes of DPP4 inhibition. Oxytocin binding mode, flexibility, and interacting residues were studied using molecular docking simulations studies. 3D-RISM calculations studies revealed that the stability of water molecules at the binding site are favorable. Finally, an experimental study using fluorescence assay revealed OXT inhibits DPP4 in a concentration-dependent manner in a significant way (p < 0.05) and possess IC50 of 110.7 nM. These new findings significantly expand the pharmaceutical application of cyclic peptides, and in specific OXT, and implicate further optimization of OXT inhibition capacity to understand the effect of DPP4 inhibition. This work highlights the development of natural cyclic peptides as future therapeutic peptides to reduce glucose levels and treat diabetes mellitus.
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Affiliation(s)
- Veera C S R Chittepu
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Av. Wilfrido Massieu S/N, Col. Unidad Profesional Adolfo López Mateos, Zacatenco, Ciudad de Mexico 07738, Mexico.
| | - Poonam Kalhotra
- Departamento de Biofísica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, CP. Ciudad de Mexico 11340, Mexico.
| | - Tzayhri Osorio-Gallardo
- Departamento de Microbiologia e Immunologia, Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autonoma de Mexico, Av. Universidad #3000, Delegacion Coyoacan, Col. Ciudad Universitaria, Ciudad de Mexico 04510, Mexico.
| | - Cristian Jiménez-Martínez
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Av. Wilfrido Massieu S/N, Col. Unidad Profesional Adolfo López Mateos, Zacatenco, Ciudad de Mexico 07738, Mexico.
| | - Raúl René Robles-de la Torre
- Centro de Investigación en Biotecnología Aplicada CIBA, Instituto Politécnico Nacional, Carretera Estatal, Tecuexcomac-Tepetitla, Km 1.5, CP. Tlaxcala 90700, Mexico.
| | - Tzayhri Gallardo-Velazquez
- Departamento de Biofísica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, CP. Ciudad de Mexico 11340, Mexico.
| | - Guillermo Osorio-Revilla
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico Nacional, Av. Wilfrido Massieu S/N, Col. Unidad Profesional Adolfo López Mateos, Zacatenco, Ciudad de Mexico 07738, Mexico.
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36
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Domhan C, Uhl P, Kleist C, Zimmermann S, Umstätter F, Leotta K, Mier W, Wink M. Replacement of l-Amino Acids by d-Amino Acids in the Antimicrobial Peptide Ranalexin and Its Consequences for Antimicrobial Activity and Biodistribution. Molecules 2019; 24:E2987. [PMID: 31426494 DOI: 10.3390/molecules24162987] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 01/09/2023] Open
Abstract
Infections caused by multidrug-resistant bacteria are a global emerging problem. New antibiotics that rely on innovative modes of action are urgently needed. Ranalexin is a potent antimicrobial peptide (AMP) produced in the skin of the American bullfrog Rana catesbeiana. Despite strong antimicrobial activity against Gram-positive bacteria, ranalexin shows disadvantages such as poor pharmacokinetics. To tackle these problems, a ranalexin derivative consisting exclusively of d-amino acids (named danalexin) was synthesized and compared to the original ranalexin for its antimicrobial potential and its biodistribution properties in a rat model. Danalexin showed improved biodistribution with an extended retention in the organisms of Wistar rats when compared to ranalexin. While ranalexin is rapidly cleared from the body, danalexin is retained primarily in the kidneys. Remarkably, both peptides showed strong antimicrobial activity against Gram-positive bacteria and Gram-negative bacteria of the genus Acinetobacter with minimum inhibitory concentrations (MICs) between 4 and 16 mg/L (1.9–7.6 µM). Moreover, both peptides showed lower antimicrobial activities with MICs ≥32 mg/L (≥15.2 µM) against further Gram-negative bacteria. The preservation of antimicrobial activity proves that the configuration of the amino acids does not affect the anticipated mechanism of action, namely pore formation.
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37
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Schnorenberg MR, Bellairs JA, Samaeekia R, Acar H, Tirrell MV, LaBelle JL. Activating the Intrinsic Pathway of Apoptosis Using BIM BH3 Peptides Delivered by Peptide Amphiphiles with Endosomal Release. Materials (Basel) 2019; 12:E2567. [PMID: 31408950 DOI: 10.3390/ma12162567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022]
Abstract
Therapeutic manipulation of the BCL-2 family using BH3 mimetics is an emerging paradigm in cancer treatment and immune modulation. For example, peptides mimicking the BIM BH3 helix can directly target the full complement of anti- and pro-apoptotic BCL-2 proteins to trigger apoptosis. This study has incorporated the potent BH3 α-helical death domain of BIM into peptide amphiphile (PA) nanostructures designed to facilitate cellular uptake and induce cell death. This study shows that these PA nanostructures are quickly incorporated into cells, are able to specifically bind BCL-2 proteins, are stable at physiologic temperatures and pH, and induce dose-dependent apoptosis in cells. The incorporation of a cathepsin B cleavable linker between the BIM BH3 peptide and the hydrophobic tail resulted in increased intracellular accumulation and mitochondrial co-localization of the BIM BH3 peptide while also improving BCL-2 family member binding and apoptotic reactivation. This PA platform represents a promising new strategy for intracellular therapeutic peptide delivery for the disruption of intracellular protein:protein interactions.
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38
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Abstract
Current research has demonstrated that small cationic amphipathic peptides have strong potential not only as antimicrobials, but also as antibiofilm agents, immune modulators, and anti-inflammatories. Although traditionally termed antimicrobial peptides (AMPs) these additional roles have prompted a shift in terminology to use the broader term host defense peptides (HDPs) to capture the multi-functional nature of these molecules. In this review, we critically examined the role of AMPs and HDPs in infectious diseases and inflammation. It is generally accepted that HDPs are multi-faceted mediators of a wide range of biological processes, with individual activities dependent on their polypeptide sequence. In this context, we explore the concept of chemical space as it applies to HDPs and hypothesize that the various functions and activities of this class of molecule exist on independent but overlapping activity landscapes. Finally, we outline several emerging functions and roles of HDPs and highlight how an improved understanding of these processes can potentially be leveraged to more fully realize the therapeutic promise of HDPs.
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Affiliation(s)
- Evan F Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Suzana K Straus
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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39
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Garton M, Corbi-Verge C, Hu Y, Nim S, Tarasova N, Sherborne B, Kim PM. Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration. Proteins 2019; 87:236-244. [PMID: 30520126 DOI: 10.1002/prot.25644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/30/2018] [Accepted: 11/29/2018] [Indexed: 11/07/2022]
Abstract
Peptide-based therapeutics are an alternative to small molecule drugs as they offer superior specificity, lower toxicity, and easy synthesis. Here we present an approach that leverages the dramatic performance increase afforded by the recent arrival of GPU accelerated thermodynamic integration (TI). GPU TI facilitates very fast, highly accurate binding affinity optimization of peptides against therapeutic targets. We benchmarked TI predictions using published peptide binding optimization studies. Prediction of mutations involving charged side-chains was found to be less accurate than for non-charged, and use of a more complex 3-step TI protocol was found to boost accuracy in these cases. Using the 3-step protocol for non-charged side-chains either had no effect or was detrimental. We use the benchmarked pipeline to optimize a peptide binding to our recently discovered cancer target: EME1. TI calculations predict beneficial mutations using both canonical and non-canonical amino acids. We validate these predictions using fluorescence polarization and confirm that binding affinity is increased. We further demonstrate that this increase translates to a significant reduction in pancreatic cancer cell viability.
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Affiliation(s)
- Michael Garton
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Yuan Hu
- Merck & Co., Inc., Kenilworth, New Jersey.,Alkermes Inc., Waltham, Massachusetts
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Nadya Tarasova
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland
| | | | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada
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40
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Yang M, Zhang Q, Wang Q, Sørensen KK, Boesen JT, Ma SY, Jensen KJ, Kwan KM, Ngo JCK, Chan HYE, Zuo Z. Brain-Targeting Delivery of Two Peptidylic Inhibitors for Their Combination Therapy in Transgenic Polyglutamine Disease Mice via Intranasal Administration. Mol Pharm 2018; 15:5781-5792. [PMID: 30392378 DOI: 10.1021/acs.molpharmaceut.8b00938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Polyglutamine diseases are a set of progressive neurodegenerative disorders caused by misfolding and aggregation of mutant CAG RNA and polyglutamin protein. To date, there is a lack of effective therapeutics that can counteract the polyglutamine neurotoxicity. Two peptidylic inhibitors, QBP1 and P3, targeting the protein and RNA toxicities, respectively, have been previously demonstrated by us with combinational therapeutic effects on the Drosophila polyglutamine disease model. However, their therapeutic efficacy has never been investigated in vivo in mammals. The current study aims to (a) develop a brain-targeting delivery system for both QBP1 and L1P3V8 (a lipidated variant of P3 with improved stability) and (b) evaluate their therapeutic effects on the R6/2 transgenic mouse model of polyglutamine disease. Compared with intravenous administration, intranasal administration of QBP1 significantly increased its brain-to-plasma ratio. In addition, employment of a chitosan-containing in situ gel for the intranasal administration of QBP1 notably improved its brain concentration for up to 10-fold. Further study on intranasal cotreatment with the optimized formulation of QBP1 and L1P3V8 in mice found no interference on the brain uptake of each other. Subsequent efficacy evaluation of 4-week daily QBP1 (16 μmol/kg) and L1P3V8 (6 μmol/kg) intranasal cotreatment in the R6/2 mice demonstrated a significant improvement on the motor coordination and explorative behavior of the disease mice, together with a full suppression on the RNA- and protein-toxicity markers in their brains. In summary, the current study developed an efficient intranasal cotreatment of the two peptidylic inhibitors, QBP1 and L1P3V8, for their brain-targeting, and such a novel therapeutic strategy was found to be effective on a transgenic polyglutamine disease mouse model.
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Affiliation(s)
- Mengbi Yang
- School of Pharmacy , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Qian Zhang
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Qianwen Wang
- School of Pharmacy , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Kasper K Sørensen
- Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Josephine T Boesen
- Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Sum Yi Ma
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Knud J Jensen
- Department of Chemistry , University of Copenhagen , Thorvaldsensvej 40 , 1871 Frederiksberg , Denmark
| | - Kin Ming Kwan
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China.,Partner State Key Laboratory of Agrobiotechnology , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Jacky Chi Ki Ngo
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Ho Yin Edwin Chan
- School of Life Sciences , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China.,Gerald Choa Neuroscience Centre , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
| | - Zhong Zuo
- School of Pharmacy , The Chinese University of Hong Kong , Shatin, Hong Kong , SAR , China
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41
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Agrawal P, Raghava GPS. Prediction of Antimicrobial Potential of a Chemically Modified Peptide From Its Tertiary Structure. Front Microbiol 2018; 9:2551. [PMID: 30416494 PMCID: PMC6212470 DOI: 10.3389/fmicb.2018.02551] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
Designing novel antimicrobial peptides is a hot area of research in the field of therapeutics especially after the emergence of resistant strains against the conventional antibiotics. In the past number of in silico methods have been developed for predicting the antimicrobial property of the peptide containing natural residues. This study describes models developed for predicting the antimicrobial property of a chemically modified peptide. Our models have been trained, tested and evaluated on a dataset that contains 948 antimicrobial and 931 non-antimicrobial peptides, containing chemically modified and natural residues. Firstly, the tertiary structure of all peptides has been predicted using software PEPstrMOD. Structure analysis indicates that certain type of modifications enhance the antimicrobial property of peptides. Secondly, a wide range of features was computed from the structure of these peptides using software PaDEL. Finally, models were developed for predicting the antimicrobial potential of chemically modified peptides using a wide range of structural features of these peptides. Our best model based on support vector machine achieve maximum MCC of 0.84 with an accuracy of 91.62% on training dataset and MCC of 0.80 with an accuracy of 89.89% on validation dataset. To assist the scientific community, we have developed a web server called "AntiMPmod" which predicts the antimicrobial property of the chemically modified peptide. The web server is present at the following link (http://webs.iiitd.edu.in/raghava/antimpmod/).
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Affiliation(s)
- Piyush Agrawal
- CSIR-Institute of Microbial Technology, Chandigarh, India.,Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
| | - Gajendra P S Raghava
- Center for Computational Biology, Indraprastha Institute of Information Technology, Delhi, New Delhi, India
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42
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Abstract
Biomolecules such as antibodies, proteins, and peptides are important tools for chemical biology and leads for drug development. They have been used to inhibit a variety of extracellular proteins, but accessing intracellular proteins has been much more challenging. In this review, we discuss diverse chemical approaches that have yielded cell-penetrant peptides and identify three distinct strategies: masking backbone amides, guanidinium group patterning, and amphipathic patterning. We summarize a growing number of large data sets, which are starting to reveal more specific design guidelines for each strategy. We also discuss advantages and disadvantages of current methods for quantifying cell penetration. Finally, we provide an overview of best-odds approaches for applying these new methods and design principles to optimize cytosolic penetration for a given bioactive peptide.
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Affiliation(s)
- Leila Peraro
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, USA
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43
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Hillman RA, Nadraws JW, Bertucci MA. The Hydrocarbon Staple & Beyond: Recent Advances Towards Stapled Peptide Therapeutics that Target Protein-Protein Interactions. Curr Top Med Chem 2018; 18:611-624. [PMID: 29773064 DOI: 10.2174/1568026618666180518095255] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 11/22/2022]
Abstract
Anomalous protein-protein interactions (PPIs) have been correlated to a variety of disease states, such as cancer, infectious disease, neurological disorders, diabetes, endocrine disorders and cardiovascular disease. Stapled peptides are an emerging intervention for these PPIs due to their improved structural rigidity and pharmacokinetic properties relative to unstapled peptides. This review details the most recent advances in the field of stapled peptide therapeutics, including the increasing variety of PPIs being targeted and types of peptide staples being employed.
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Affiliation(s)
- Robert A Hillman
- Department of Chemistry, Moravian College, Bethlehem, PA 18018, United States
| | - Jonathan W Nadraws
- Department of Chemistry, Moravian College, Bethlehem, PA 18018, United States
| | - Michael A Bertucci
- Department of Chemistry, Moravian College, Bethlehem, PA 18018, United States
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44
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Abstract
The Gram-negative bacterium Aggregatibacter actinomycetemcomitans, commonly associated with localized aggressive periodontitis (LAP), secretes an RTX (repeats-in-toxin) protein leukotoxin (LtxA) that targets human white blood cells, an interaction that is driven by its recognition of the lymphocyte function-associated antigen-1 (LFA-1) integrin. In this study, we report on the inhibition of LtxA-LFA-1 binding as an antivirulence strategy to inhibit LtxA-mediated cytotoxicity. Specifically, we designed and synthesized peptides corresponding to the reported LtxA binding domain on LFA-1 and characterized their capability to inhibit LtxA binding to LFA-1 and subsequent cytotoxic activity in human immune cells. We found that several of these peptides, corresponding to sequential β-strands in the LtxA-binding domain of LFA-1, inhibit LtxA activity, demonstrating the effectiveness of this approach. Further investigations into the mechanism by which these peptides inhibit LtxA binding to LFA-1 reveal a correlation between toxin-peptide affinity and LtxA-mediated cytotoxicity, leading to a diminished association between LtxA and LFA-1 on the cell membrane. Our results demonstrate the possibility of using target-based peptides to inhibit LtxA activity, and we expect that a similar approach could be used to hinder the activity of other RTX toxins.
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Affiliation(s)
- Eric Krueger
- Department of Chemical and Biomolecular Engineering, Lehigh University, Iacocca Hall, Room B323, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
| | - Shannon Hayes
- Department of Chemical and Biomolecular Engineering, Lehigh University, Iacocca Hall, Room B323, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
| | - En Hyung Chang
- Department of Chemical and Biomolecular Engineering, Lehigh University, Iacocca Hall, Room B323, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
| | - Shailagne Yutuc
- Department of Chemical and Biomolecular Engineering, Lehigh University, Iacocca Hall, Room B323, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
| | - Angela C. Brown
- Department of Chemical and Biomolecular Engineering, Lehigh University, Iacocca Hall, Room B323, 111 Research Drive, Bethlehem, Pennsylvania 18015, United States
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45
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Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GPS. Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. Brief Bioinform 2017; 18:467-478. [PMID: 27016393 DOI: 10.1093/bib/bbw025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/19/2022] Open
Abstract
The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using the whole pathogen responsible for the disease. In the post-genomic era, a major challenge is to identify antigenic regions or epitopes that can stimulate different arms of the immune system. In the past two decades, numerous methods and databases have been developed for designing vaccine or immunotherapy against various pathogen-causing diseases. This review describes various computational resources important for designing subunit vaccines or epitope-based immunotherapy. First, different immunological databases are described that maintain epitopes, antigens and vaccine targets. This is followed by in silico tools used for predicting linear and conformational B-cell epitopes required for activating humoral immunity. Finally, information on T-cell epitope prediction methods is provided that includes indirect methods like prediction of Major Histocompatibility Complex and transporter-associated protein binders. Different studies for validating the predicted epitopes are also examined critically. This review enlists novel in silico resources and tools available for predicting humoral and cell-mediated immune potential. These predicted epitopes could be used for designing epitope-based vaccines or immunotherapy as they may activate the adaptive immunity. Authors emphasized the need to develop tools for the prediction of adjuvants to activate innate and adaptive immune system simultaneously. In addition, attention has also been given to novel prediction methods to predict general therapeutic properties of peptides like half-life, cytotoxicity and immune toxicity.
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46
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Abstract
We are introducing a new approach to evaluate cellular uptake of drugs and drug candidates into living cells. The approach is based on converting the protein target of a given class of compounds into a fluorescent biosensor. By measuring the binding of different compounds to their cognate biosensor in live cells and comparing these values to those measured in vitro, their cellular uptake and concentrations can be ranked. We demonstrate that our strategy enables the evaluation of the cellular uptake into the cytosol of 2 classes of inhibitors using two different sensor designs; first, sensors comprising the self-labeling protein SNAP conjugated with a chemically modified inhibitor shown for inhibitors of the enzyme human carbonic anhydrase II; and a label-free sensor for inhibitors of protein-protein interactions demonstrated for the protein pair p53-HDM2.
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Affiliation(s)
- Silvia Scarabelli
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne CH-1015, Switzerland
- National Centre of Competence in Research in Chemical Biology, Lausanne, CH-1015, Switzerland
| | - Kui Thong Tan
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne CH-1015, Switzerland
- National Centre of Competence in Research in Chemical Biology, Lausanne, CH-1015, Switzerland
| | - Rudolf Griss
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne CH-1015, Switzerland
- National Centre of Competence in Research in Chemical Biology, Lausanne, CH-1015, Switzerland
| | - Ruud Hovius
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne CH-1015, Switzerland
- National Centre of Competence in Research in Chemical Biology, Lausanne, CH-1015, Switzerland
| | | | - Thomas Vorherr
- Novartis Institutes for BioMedical Research, Basel, CH-4056, Switzerland
| | - Kai Johnsson
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne CH-1015, Switzerland
- National Centre of Competence in Research in Chemical Biology, Lausanne, CH-1015, Switzerland
- Max-Planck-Institute for Medical Research, Department of Chemical
Biology, 69120 Heidelberg, Germany
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47
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Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR. Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angew Chem Int Ed Engl 2017; 56:524-529. [PMID: 27918136 PMCID: PMC5291322 DOI: 10.1002/anie.201609427] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/18/2016] [Indexed: 02/04/2023]
Abstract
There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1β, in five high- and low-HNF1β-expressing CCC lines. To inhibit the protein function, cell-permeable, non-helical constrained proteomimetics to target the HNF1β-importin α protein-protein interaction were designed, guided by X-ray crystallographic data and molecular dynamics simulations. In this way, we developed the first reported series of constrained peptide nuclear import inhibitors. Importantly, this general approach may be extended to other transcription factors.
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Affiliation(s)
- Mareike M. Wiedmann
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
| | - Yuteng Wu
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Shintaro Aibara
- SciLifeLabTomtebodavägen 23A171 65 SolnaStockholmSweden
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Wenshu Xu
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Hannah F. Sore
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
- School of Biological SciencesNanyang Technological University60 Nanyang DriveSingapore637551Singapore
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Laura Itzhaki
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Murray Stewart
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - James D. Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - David R. Spring
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
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Sugamori Y, Mise-Omata S, Maeda C, Aoki S, Tabata Y, Murali R, Yasuda H, Udagawa N, Suzuki H, Honma M, Aoki K. Peptide drugs accelerate BMP-2-induced calvarial bone regeneration and stimulate osteoblast differentiation through mTORC1 signaling. Bioessays 2016; 38:717-25. [PMID: 27345003 PMCID: PMC5094554 DOI: 10.1002/bies.201600104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Both W9 and OP3‐4 were known to bind the receptor activator of NF‐κB ligand (RANKL), inhibiting osteoclastogenesis. Recently, both peptides were shown to stimulate osteoblast differentiation; however, the mechanism underlying the activity of these peptides remains to be clarified. A primary osteoblast culture showed that rapamycin, an mTORC1 inhibitor, which was recently demonstrated to be an important serine/threonine kinase for bone formation, inhibited the peptide‐induced alkaline phosphatase activity. Furthermore, both peptides promoted the phosphorylation of Akt and S6K1, an upstream molecule of mTORC1 and the effector molecule of mTORC1, respectively. In the in vivo calvarial defect model, W9 and OP3‐4 accelerated BMP‐2‐induced bone formation to a similar extent, which was confirmed by histomorphometric analyses using fluorescence images of undecalcified sections. Our data suggest that these RANKL‐binding peptides could stimulate the mTORC1 activity, which might play a role in the acceleration of BMP‐2‐induced bone regeneration by the RANKL‐binding peptides.
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Affiliation(s)
- Yasutaka Sugamori
- Department of Bio-Matrix (Pharmacology), Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Setsuko Mise-Omata
- Department of Bio-Matrix (Pharmacology), Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chizuko Maeda
- Department of Bio-Matrix (Pharmacology), Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeki Aoki
- Faculty of Medicine, Department of Pharmacy, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan
| | - Yasuhiko Tabata
- Department of Biomaterials, Field of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ramachandran Murali
- Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hisataka Yasuda
- Nagahama Institute for Biochemical Science, Oriental Yeast Co. Ltd., Shiga, Japan
| | - Nobuyuki Udagawa
- Department of Biochemistry, Matsumoto Dental University, Nagano, Japan
| | - Hiroshi Suzuki
- Faculty of Medicine, Department of Pharmacy, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan
| | - Masashi Honma
- Faculty of Medicine, Department of Pharmacy, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan.,Faculty of Medicine, Department of Pharmacology and Pharmacokinetics, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Aoki
- Department of Bio-Matrix (Pharmacology), Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Verdes A, Anand P, Gorson J, Jannetti S, Kelly P, Leffler A, Simpson D, Ramrattan G, Holford M. From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins. Toxins (Basel) 2016; 8:117. [PMID: 27104567 PMCID: PMC4848642 DOI: 10.3390/toxins8040117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022] Open
Abstract
Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, identifying bioactive venom peptides remains a significant challenge. In this review we describe our particular venomics strategy for the discovery, characterization, and optimization of Terebridae venom peptides, teretoxins. Our strategy reflects the scientific path from mollusks to medicine in an integrative sequential approach with the following steps: (1) delimitation of venomous Terebridae lineages through taxonomic and phylogenetic analyses; (2) identification and classification of putative teretoxins through omics methodologies, including genomics, transcriptomics, and proteomics; (3) chemical and recombinant synthesis of promising peptide toxins; (4) structural characterization through experimental and computational methods; (5) determination of teretoxin bioactivity and molecular function through biological assays and computational modeling; (6) optimization of peptide toxin affinity and selectivity to molecular target; and (7) development of strategies for effective delivery of venom peptide therapeutics. While our research focuses on terebrids, the venomics approach outlined here can be applied to the discovery and characterization of peptide toxins from any venomous taxa.
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Affiliation(s)
- Aida Verdes
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Prachi Anand
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Juliette Gorson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
| | - Stephen Jannetti
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Patrick Kelly
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
| | - Abba Leffler
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine 550 1st Avenue, New York, NY 10016, USA.
| | - Danny Simpson
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- Tandon School of Engineering, New York University 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Girish Ramrattan
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Mandë Holford
- Hunter College, The City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The Graduate Center, City University of New York, 365 5th Ave, New York, NY 10016, USA.
- Sackler Institute for Comparative Genomics, Invertebrate Zoology, American Museum of Natural History, Central Park West & 79th St, New York, NY 10024, USA.
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50
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Kelly P, Anand P, Uvaydov A, Chakravartula S, Sherpa C, Pires E, O'Neil A, Douglas T, Holford M. Developing a Dissociative Nanocontainer for Peptide Drug Delivery. Int J Environ Res Public Health 2015; 12:12543-55. [PMID: 26473893 PMCID: PMC4626985 DOI: 10.3390/ijerph121012543] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/23/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022]
Abstract
The potency, selectivity, and decreased side effects of bioactive peptides have propelled these agents to the forefront of pharmacological research. Peptides are especially promising for the treatment of neurological disorders and pain. However, delivery of peptide therapeutics often requires invasive techniques, which is a major obstacle to their widespread application. We have developed a tailored peptide drug delivery system in which the viral capsid of P22 bacteriophage is modified to serve as a tunable nanocontainer for the packaging and controlled release of bioactive peptides. Recent efforts have demonstrated that P22 nanocontainers can effectively encapsulate analgesic peptides and translocate them across blood-brain-barrier (BBB) models. However, release of encapsulated peptides at their target site remains a challenge. Here a Ring Opening Metathesis Polymerization (ROMP) reaction is applied to trigger P22 nanocontainer disassembly under physiological conditions. Specifically, the ROMP substrate norbornene (5-Norbornene-2-carboxylic acid) is conjugated to the exterior of a loaded P22 nanocontainer and Grubbs II Catalyst is used to trigger the polymerization reaction leading to nanocontainer disassembly. Our results demonstrate initial attempts to characterize the ROMP-triggered release of cargo peptides from P22 nanocontainers. This work provides proof-of-concept for the construction of a triggerable peptide drug delivery system using viral nanocontainers.
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Affiliation(s)
- Patrick Kelly
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Prachi Anand
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Alexander Uvaydov
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Srinivas Chakravartula
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Chhime Sherpa
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Elena Pires
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
| | - Alison O'Neil
- Stem Cell and Regenerative Biology Department, Harvard University, 7 Divinity Ave, Cambridge, MA 02138, USA.
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA.
| | - Mandë Holford
- Hunter College and The Graduate Center, City University of New York, Belfer Research Building, 413 E. 69th Street, New York, NY 10021, USA.
- The American Museum of Natural History, Central Park West & 79th Street, New York, NY 10024, USA.
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