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Dokuz S, Tasdurmazli S, Acar T, Duran GN, Ozdemir C, Ozbey U, Ozbil M, Karadayi S, Bayrak OF, Derman S, Chen JYS, Ozbek T. Evaluation of Bacteriophage ϕ11 host recognition protein and its host-binding peptides for diagnosing/targeting Staphylococcus aureus infections. Int J Antimicrob Agents 2024; 64:107230. [PMID: 38824973 DOI: 10.1016/j.ijantimicag.2024.107230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
BACKGROUND Evaluating the potential of using both synthetic and biological products as targeting agents for the diagnosis, imaging, and treatment of infections due to particularly antibiotic-resistant pathogens is important for controlling infections. This study examined the interaction between Gp45, a receptor-binding protein of the ϕ11 lysogenic phage, and its host Staphylococcus aureus (S. aureus), a common cause of nosocomial infections. METHODS Using molecular dynamics and docking simulations, this study identified the peptides that bind to S. aureus wall teichoic acids via Gp45. It compared the binding affinity of Gp45 and the two highest-scoring peptide sequences (P1 and P3) and their scrambled forms using microscopy, spectroscopy, and ELISA. RESULTS It was found that rGp45 (recombinant Gp45) and chemically synthesised P1 had a higher binding affinity for S. aureus compared with all other peptides, except for Escherichia coli. Furthermore, rGp45 had a capture efficiency of > 86%; P1 had a capture efficiency of > 64%. CONCLUSION These findings suggest that receptor-binding proteins such as rGp45, which provide a critical initiation of the phage life cycle for host adsorption, might play an important role in the diagnosis, imaging, and targeting of bacterial infections. Studying such proteins could accordingly enable the development of effective strategies for controlling infections.
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Affiliation(s)
- Senanur Dokuz
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Semra Tasdurmazli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Tayfun Acar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Gizem Nur Duran
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Cilem Ozdemir
- Department of Medical Biology, Health Sciences Institution, Mugla Sitki Kocman University, Mugla, Turkey
| | - Utku Ozbey
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Mehmet Ozbil
- Institute of Biotechnology, Gebze Technical University, Kocaeli, Turkey
| | - Sukriye Karadayi
- Department of Medical Laboratory Techniques, Vocational School of Health Services, Altınbas University, Istanbul, Turkey
| | - Omer Faruk Bayrak
- Department of Medical Genetics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Serap Derman
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Istanbul, Turkey
| | - John Yu-Shen Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tulin Ozbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey.
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Buonocore M, Grimaldi M, Santoro A, Covelli V, Marino C, Napolitano E, Novi S, Tecce MF, Ciaglia E, Montella F, Lopardo V, Perugini V, Santin M, D’Ursi AM. Exploiting the Features of Short Peptides to Recognize Specific Cell Surface Markers. Int J Mol Sci 2023; 24:15610. [PMID: 37958593 PMCID: PMC10650159 DOI: 10.3390/ijms242115610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Antibodies are the macromolecules of choice to ensure specific recognition of biomarkers in biological assays. However, they present a range of shortfalls including a relatively high production cost and limited tissue penetration. Peptides are relatively small molecules able to reproduce sequences of highly specific paratopes and, although they have less biospecificity than antibodies, they offer advantages like ease of synthesis, modifications of their amino acid sequences and tagging with fluorophores and other molecules required for detection. This work presents a strategy to design peptide sequences able to recognize the CD44 hyaluronic acid receptor present in the plasmalemma of a range of cells including human bone marrow stromal mesenchymal cells. The protocol of identification of the optimal amino acid sequence was based on the combination of rational design and in silico methodologies. This protocol led to the identification of two peptide sequences which were synthesized and tested on human bone marrow mesenchymal stromal cells (hBM-MSCs) for their ability to ensure specific binding to the CD44 receptor. Of the two peptides, one binds CD44 with sensitivity and selectivity, thus proving its potential to be used as a suitable alternative to this antibody in conventional immunostaining. In the context of regenerative medicine, the availability of this peptide could be harnessed to functionalize tissue engineering scaffolds to anchor stem cells as well as to be integrated into systems such as cell sorters to efficiently isolate MSCs from biological samples including various cell subpopulations. The data here reported can represent a model for developing peptide sequences able to recognize hBM-MSCs and other types of cells and for their integration in a range of biomedical applications.
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Affiliation(s)
- Michela Buonocore
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Chemical Sciences, University of Naples Federico II, 80138 Naples, Italy
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Angelo Santoro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Scuola di Specializzazione in Farmacia Ospedaliera, University of Salerno, 84084 Fisciano, Italy
| | - Verdiana Covelli
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, 80138 Naples, Italy
| | - Carmen Marino
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Enza Napolitano
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Sara Novi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Mario Felice Tecce
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
| | - Elena Ciaglia
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Francesco Montella
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valentina Lopardo
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy; (E.C.); (F.M.); (V.L.)
| | - Valeria Perugini
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Matteo Santin
- Centre for Regenerative Medicine and Devices, School of Applied Sciences, University of Brighton, Brighton BN2 4AT, UK; (V.P.); (M.S.)
| | - Anna Maria D’Ursi
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy or (M.B.); (M.G.); (A.S.); or (V.C.); (C.M.); (E.N.); (S.N.); (M.F.T.)
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3
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Santoro A, Buonocore M, Grimaldi M, Napolitano E, D’Ursi AM. Monitoring the Conformational Changes of the Aβ(25-35) Peptide in SDS Micelles: A Matter of Time. Int J Mol Sci 2023; 24:ijms24020971. [PMID: 36674488 PMCID: PMC9867351 DOI: 10.3390/ijms24020971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/28/2022] [Accepted: 12/31/2022] [Indexed: 01/07/2023] Open
Abstract
Alzheimer's disease is a neurodegenerative disease characterized by the formation of amyloid plaques constituted prevalently by amyloid peptides. Due to the well-known challenges related to the study in solution of these peptides, several membrane-mimicking systems such as micelle constituted by detergent-i.e., DPC and SDS-have been deeply investigated. Additionally, the strategy of studying short fragments instead of the full-length peptide turned out to be advantageous in exploring the structural properties of the different moieties in Aβ in order to reproduce its pathologic effects. Several studies reveal that among Aβ fragments, Aβ(25-35) is the shortest fragment able to reproduce the aggregation process. To enrich the structural data currently available, in the present work we decided to evaluate the conformational changes adopted by Aβ(25-35) in SDS combining CD and NMR spectroscopies at different times. From the solved structures, it emerges that Aβ(25-35) passes from an unordered conformation at the time of the constitution of the system to a more ordered and energetically favorable secondary structure at day 7, which is kept for 2 weeks. These preliminary data suggest that a relatively long time affects the kinetic in the aggregation process of Aβ(25-35) in a micellar system, favoring the stabilization and the formation of a soluble helix conformation.
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Affiliation(s)
- Angelo Santoro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
- Department of Pharmacy, Scuola di Specializzazione in Farmacia Ospedaliera, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Michela Buonocore
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
- Department of Veterinary Pathology, University of Naples Federico II, Via Federico Delpino 1, 80137 Naples, Italy
| | - Manuela Grimaldi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Enza Napolitano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy
| | - Anna Maria D’Ursi
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
- Correspondence:
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Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site. Heliyon 2022; 8:e11568. [PMID: 36406731 PMCID: PMC9663143 DOI: 10.1016/j.heliyon.2022.e11568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an RNA virus identified as the cause of the coronavirus outbreak in December 2019 (COVID-19). Like all the RNA viruses, SARS-CoV-2 constantly evolves through mutations in its genome, accumulating 1–2 nucleotide changes every month, giving the virus a selective advantage through enhanced transmissibility, greater pathogenicity, and the possibility of circumventing immunity previously acquired by an individual either by natural infection or by vaccination. Several SARS-CoV-2 variants of concern (VoC) have been identified, among which we find Alpha (Lineage B.1.1.7), Beta (Lineage B.1.351), and Gamma (Lineage P.1) variants. Most of the mutations occur in the spike (S) protein, a surface glycoprotein that plays a crucial role in viral infection; the S protein binds the host cell receptor, the angiotensin-converting enzyme of type 2 (ACE2) via the receptor binding domain (RBD) and catalyzes the fusion of the viral membrane with the host cell. In this work, we present the development of a simplified system that would afford to study the change in the SARS-CoV-2 S RBD/ACE2 binding related to the frequent mutations. In particular, we synthesized and studied the structure of short amino acid sequences, mimicking the two proteins’ critical portions. Variations in the residues were easily managed through the one-point alteration of the sequences. Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies provide insights into ACE2 and SARS-CoV-2 S RBD structure with its related three variants (Alpha, Beta, and Gamma). Spectroscopy data supported by molecular dynamics lead to the description of an ACE2/RBD binding model in which the effect of a single amino acid mutation in changing the binding of S protein to the ACE2 receptor is predictable.
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Santa-Coloma TA. Overlapping synthetic peptides as a tool to map protein-protein interactions ̶ FSH as a model system of nonadditive interactions. Biochim Biophys Acta Gen Subj 2022; 1866:130153. [DOI: 10.1016/j.bbagen.2022.130153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 10/18/2022]
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6
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Liu X, Zhang Q, Knoll W, Liedberg B, Wang Y. Rational Design of Functional Peptide-Gold Hybrid Nanomaterials for Molecular Interactions. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000866. [PMID: 32743897 DOI: 10.1002/adma.202000866] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/21/2020] [Indexed: 05/12/2023]
Abstract
Gold nanoparticles (AuNPs) have been extensively used for decades in biosensing-related development due to outstanding optical properties. Peptides, as newly realized functional biomolecules, are promising candidates of replacing antibodies, receptors, and substrates for specific molecular interactions. Both peptides and AuNPs are robust and easily synthesized at relatively low cost. Hence, peptide-AuNP-based bio-nano-technological approaches have drawn increasing interest, especially in the field of molecular targeting, cell imaging, drug delivery, and therapy. Many excellent works in these areas have been reported: demonstrating novel ideas, exploring new targets, and facilitating advanced diagnostic and therapeutic technologies. Importantly, some of them also have been employed to address real practical problems, especially in remote and less privileged areas. This contribution focuses on the application of peptide-gold hybrid nanomaterials for various molecular interactions, especially in biosensing/diagnostics and cell targeting/imaging, as well as for the development of highly active antimicrobial/antifouling coating strategies. Rationally designed peptide-gold nanomaterials with functional properties are discussed along with future challenges and opportunities.
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Affiliation(s)
- Xiaohu Liu
- School of Biomedical Engineering, School of Ophthalmology & Optometry, Wenzhou Medical University, Xueyuan Road 270, Wenzhou, 325027, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Xinsan Road 16, Wenzhou, 325001, China
| | - Qingwen Zhang
- School of Biomedical Engineering, School of Ophthalmology & Optometry, Wenzhou Medical University, Xueyuan Road 270, Wenzhou, 325027, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Xinsan Road 16, Wenzhou, 325001, China
| | - Wolfgang Knoll
- Austrian Institute of Technology, Giefinggasse 4, Vienna, 1210, Austria
| | - Bo Liedberg
- Centre for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yi Wang
- School of Biomedical Engineering, School of Ophthalmology & Optometry, Wenzhou Medical University, Xueyuan Road 270, Wenzhou, 325027, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Xinsan Road 16, Wenzhou, 325001, China
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7
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Wu KJ, Lei PM, Liu H, Wu C, Leung CH, Ma DL. Mimicking Strategy for Protein-Protein Interaction Inhibitor Discovery by Virtual Screening. Molecules 2019; 24:molecules24244428. [PMID: 31817099 PMCID: PMC6943618 DOI: 10.3390/molecules24244428] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
As protein–protein interactions (PPIs) are highly involved in most cellular processes, the discovery of PPI inhibitors that mimic the structure of the natural protein partners is a promising strategy toward the discovery of PPI inhibitors. In this review, we discuss recent advances in the application of virtual screening for identifying mimics of protein partners. The classification and function of the mimicking protein partner inhibitor discovery by virtual screening are described. We anticipate that this review would be of interest to medicinal chemists and chemical biologists working in the field of protein–protein interaction inhibitors or probes.
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Affiliation(s)
- Ke-Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; (K.-J.W.); (P.-M.L.)
| | - Pui-Man Lei
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; (K.-J.W.); (P.-M.L.)
| | - Hao Liu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China; (H.L.); (C.W.)
| | - Chun Wu
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China; (H.L.); (C.W.)
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China; (K.-J.W.); (P.-M.L.)
- Correspondence: (C.-H.L.); (D.-L.M.); Tel.: +(853)-8822-4688 (C.-H.L.); +(852)-3411-7075 (D.-L.M.)
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China; (H.L.); (C.W.)
- Correspondence: (C.-H.L.); (D.-L.M.); Tel.: +(853)-8822-4688 (C.-H.L.); +(852)-3411-7075 (D.-L.M.)
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Ringel O, Vieillard V, Debré P, Eichler J, Büning H, Dietrich U. The Hard Way towards an Antibody-Based HIV-1 Env Vaccine: Lessons from Other Viruses. Viruses 2018; 10:v10040197. [PMID: 29662026 PMCID: PMC5923491 DOI: 10.3390/v10040197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
Although effective antibody-based vaccines have been developed against multiple viruses, such approaches have so far failed for the human immunodeficiency virus type 1 (HIV-1). Despite the success of anti-retroviral therapy (ART) that has turned HIV-1 infection into a chronic disease and has reduced the number of new infections worldwide, a vaccine against HIV-1 is still urgently needed. We discuss here the major reasons for the failure of “classical” vaccine approaches, which are mostly due to the biological properties of the virus itself. HIV-1 has developed multiple mechanisms of immune escape, which also account for vaccine failure. So far, no vaccine candidate has been able to induce broadly neutralizing antibodies (bnAbs) against primary patient viruses from different clades. However, such antibodies were identified in a subset of patients during chronic infection and were shown to protect from infection in animal models and to reduce viremia in first clinical trials. Their detailed characterization has guided structure-based reverse vaccinology approaches to design better HIV-1 envelope (Env) immunogens. Furthermore, conserved Env epitopes have been identified, which are promising candidates in view of clinical applications. Together with new vector-based technologies, considerable progress has been achieved in recent years towards the development of an effective antibody-based HIV-1 vaccine.
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Affiliation(s)
- Oliver Ringel
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany.
| | - Vincent Vieillard
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, 75013 Paris, France.
| | - Patrice Debré
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, 75013 Paris, France.
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, 91058 Erlangen, Germany.
| | - Hildegard Büning
- Laboratory for Infection Biology & Gene Transfer, Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany.
- German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.
| | - Ursula Dietrich
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt, Germany.
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Haußner C, Lach J, Eichler J. Synthetic antibody mimics for the inhibition of protein-ligand interactions. Curr Opin Chem Biol 2017; 40:72-77. [PMID: 28735229 DOI: 10.1016/j.cbpa.2017.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/31/2017] [Accepted: 07/03/2017] [Indexed: 12/22/2022]
Abstract
The rational/structure-based design and/or combinatorial development of molecules capable of selectively binding to a protein, represents a promising strategy for a range of biomedical applications, in particular the inhibition of disease-associated protein-ligand interactions. The design of such protein binding molecules is often based on an antibody against the target protein, or involves the generation of smaller molecules that retain the binding characteristics of the antibody. Alternatively, protein binding molecules can be selected from protein libraries based on small, stably folded protein scaffolds presenting flexible loops, which are randomized in the libraries. In addition to recombinantly synthesized molecules, synthetic antibody paratope mimetic peptides have emerged as promising molecules for the design of antibody mimics.
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Affiliation(s)
- Christina Haußner
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Johannes Lach
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstr. 19, 91052 Erlangen, Germany.
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Haußner C, Damm D, Nirschl S, Rohrhofer A, Schmidt B, Eichler J. Peptide Paratope Mimics of the Broadly Neutralizing HIV-1 Antibody b12. Chembiochem 2017; 18:647-653. [DOI: 10.1002/cbic.201600621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Christina Haußner
- Department of Chemistry and Pharmacy; University of Erlangen-Nürnberg; Schuhstrasse 19 91052 Erlangen Germany
| | - Dominik Damm
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Sandra Nirschl
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Barbara Schmidt
- Institute of Medical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
- Institute of Clinical Microbiology and Hygiene; University of Regensburg; Franz-Josef-Strauss-Allee 11 93053 Regensburg Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy; University of Erlangen-Nürnberg; Schuhstrasse 19 91052 Erlangen Germany
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Leo N, Liu J, Archbold I, Tang Y, Zeng X. Ionic Strength, Surface Charge, and Packing Density Effects on the Properties of Peptide Self-Assembled Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:2050-2058. [PMID: 28135097 DOI: 10.1021/acs.langmuir.6b04038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The various environmental parameters of packing density, ionic strength, and solution charge were examined for their effects on the properties of the immobilized peptide mimotope CH19 (CGSGSGSQLGPYELWELSH) that binds with the therapeutic antibody Trastuzumab (Herceptin) on a gold substrate. The immobilization of CH19 onto gold was examined with a quartz crystal microbalance (QCM). The QCM data showed the presence of intermolecular interactions resulting in the increase of viscoelastic properties of the peptide self-assembled monolayer (SAM). The CH19 SAM was diluted with CS7 (CGSGSGS) to decrease the packing density as CH19/CS7. The packing density and ionic strength parameters were evaluated by atomic force microscopy (AFM), ellipsometry, and QCM. AFM and ellipsometry showed a distinct conformational difference between CH19 and CH19/CS7, indicating a relationship between packing density and conformational state of the immobilized peptide. The CH19 SAM thickness was 40 Å with a rough topology, while the CH19/CS7 SAM thickness was 20 Å with a smooth topology. The affinity studies showed that the affinity of CH19 and CH19/CS7 to Trastuzumab were both on the order of 107 M-1 in undiluted PBS buffer, while the dilution of the buffer by 1000× increased both SAMs affinities to Trastuzumab to the order of 1015 M-2 and changed the binding behavior from noncooperative to cooperative binding. This indicated that ionic strength had a more pronounced effect on binding properties of the CH19 SAM than packing density. Electrochemical impedance spectroscopy (EIS) was conducted on the CH19/CS7 SAM, which showed an increase in impedance after each EIS measurement cycle. Cyclic voltammetry on the CH19/CS7 SAM decreased impedance to near initial values. The impact of the packing density, buffer ionic strength, and local charge perturbation of the peptide SAM properties was interpreted based on the titratable sites in CH19 that could participate in the proton transfer and water equilibrium.
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Affiliation(s)
- Norman Leo
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Juan Liu
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ian Archbold
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Yongan Tang
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Xiangqun Zeng
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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12
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Short peptides interfering with signaling pathways as new therapeutic tools for cancer treatment. Future Med Chem 2017; 9:199-221. [PMID: 28111982 DOI: 10.4155/fmc-2016-0189] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Short peptides have many advantages, such as low molecular weight, selectivity for a specific target, organelles or cells with minimal toxicity. We describe properties of short peptides, which interfere with communication networks in tumor cells and within microenvironment of malignant gliomas, the most common brain tumors. We focus on ligand/receptor axes and intracellular signaling pathways critical for gliomagenesis that could be targeted with interfering peptides. We review structures and efficacy of organelle-specific and cell-penetrating peptides and describe diverse chemical modifications increasing proteolytic stability and protecting synthetic peptides against degradation. We report results of application of short peptides in glioma therapy clinical trials, their rises and falls. The most advanced examples of therapeutics such as short interfering peptides combined with cell-penetrating peptides that show good effectiveness in disease models are presented. It is foreseen that identification of peptides with better clinical properties may improve their success rates in clinical trials.
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13
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Groß A, Hashimoto C, Sticht H, Eichler J. Synthetic Peptides as Protein Mimics. Front Bioeng Biotechnol 2016; 3:211. [PMID: 26835447 PMCID: PMC4717299 DOI: 10.3389/fbioe.2015.00211] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/22/2015] [Indexed: 12/21/2022] Open
Abstract
The design and generation of molecules capable of mimicking the binding and/or functional sites of proteins represents a promising strategy for the exploration and modulation of protein function through controlled interference with the underlying molecular interactions. Synthetic peptides have proven an excellent type of molecule for the mimicry of protein sites because such peptides can be generated as exact copies of protein fragments, as well as in diverse chemical modifications, which includes the incorporation of a large range of non-proteinogenic amino acids as well as the modification of the peptide backbone. Apart from extending the chemical and structural diversity presented by peptides, such modifications also increase the proteolytic stability of the molecules, enhancing their utility for biological applications. This article reviews recent advances by this and other laboratories in the use of synthetic protein mimics to modulate protein function, as well as to provide building blocks for synthetic biology.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Chie Hashimoto
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
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14
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Hashimoto C, Eichler J. Turning Peptide Ligands into Small-Molecule Inhibitors of Protein-Protein Interactions. Chembiochem 2015; 16:1855-1856. [PMID: 26147884 DOI: 10.1002/cbic.201500298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 11/07/2022]
Abstract
Proline makeover: Truncation and extensive chemical modification of a peptide ligand yielded a biologically active, cell-permeable, peptidomimetic, small-molecule inhibitor of a protein-protein interaction. A key step in this transformation was the replacement of a tetraproline motif by two conformationally constrained diproline units that retain the molecule's PPII helix.
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Affiliation(s)
- Chie Hashimoto
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department Chemie und Pharmazie, Schuhstrasse 19, 91052 Erlangen (Germany)
| | - Jutta Eichler
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Department Chemie und Pharmazie, Schuhstrasse 19, 91052 Erlangen (Germany)
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15
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Watanabe H, Honda S. Adaptive Assembly: Maximizing the Potential of a Given Functional Peptide with a Tailor-Made Protein Scaffold. ACTA ACUST UNITED AC 2015; 22:1165-73. [PMID: 26299673 DOI: 10.1016/j.chembiol.2015.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/18/2015] [Accepted: 07/05/2015] [Indexed: 01/28/2023]
Abstract
Protein engineering that exploits known functional peptides holds great promise for generating novel functional proteins. Here we propose a combinatorial approach, termed adaptive assembly, which provides a tailor-made protein scaffold for a given functional peptide. A combinatorial library was designed to create a tailor-made scaffold, which was generated from β hairpins derived from a 10-residue minimal protein "chignolin" and randomized amino acid sequences. We applied adaptive assembly to a peptide with low affinity for the Fc region of human immunoglobulin G, generating a 54-residue protein AF.p17 with a 40,600-fold enhanced affinity. The crystal structure of AF.p17 complexed with the Fc region revealed that the scaffold fixed the active conformation with a unique structure composed of a short α helix, β hairpins, and a loop-like structure. Adaptive assembly can take full advantage of known peptides as assets for generating novel functional proteins.
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Affiliation(s)
- Hideki Watanabe
- Biomedical Research Institute, the National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Shinya Honda
- Biomedical Research Institute, the National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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16
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Kafurke U, Erijman A, Aizner Y, Shifman JM, Eichler J. Synthetic peptides mimicking the binding site of human acetylcholinesterase for its inhibitor fasciculin 2. J Pept Sci 2015. [DOI: 10.1002/psc.2797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Uwe Kafurke
- Department of Chemistry and Pharmacy; University of Erlangen-Nuremberg; Schuhstr. 19 91052 Erlangen Germany
| | - Ariel Erijman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Yonatan Aizner
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Julia M. Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Jutta Eichler
- Department of Chemistry and Pharmacy; University of Erlangen-Nuremberg; Schuhstr. 19 91052 Erlangen Germany
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17
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Interactions of HIV-1 proteins as targets for developing anti-HIV-1 peptides. Future Med Chem 2015; 7:1055-77. [DOI: 10.4155/fmc.15.46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Protein–protein interactions (PPI) are essential in every step of the HIV replication cycle. Mapping the interactions between viral and host proteins is a fundamental target for the design and development of new therapeutics. In this review, we focus on rational development of anti-HIV-1 peptides based on mapping viral–host and viral–viral protein interactions all across the HIV-1 replication cycle. We also discuss the mechanism of action, specificity and stability of these peptides, which are designed to inhibit PPI. Some of these peptides are excellent tools to study the mechanisms of PPI in HIV-1 replication cycle and for the development of anti-HIV-1 drug leads that modulate PPI.
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18
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Cho PY, Joshi G, Boersma MD, Johnson JA, Murphy RM. A Cyclic Peptide Mimic of the β-Amyloid Binding Domain on Transthyretin. ACS Chem Neurosci 2015; 6:778-89. [PMID: 25713928 DOI: 10.1021/cn500272a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Self-association of β-amyloid (Aβ) into oligomers and fibrils is associated with Alzheimer's disease (AD), motivating the search for compounds that bind to and inhibit Aβ oligomerization and/or neurotoxicity. Peptides are an attractive class of such compounds, with potential advantages over small molecules in affinity and specificity. Self-complementation and peptide library screening are two strategies that have been employed in the search for peptides that bind to Aβ. Alternatively, one could design Aβ-binding peptides based on knowledge of complementary binding proteins. One candidate protein, transthyretin (TTR), binds Aβ, inhibits aggregation, and reduces its toxicity. Previously, strand G of TTR was identified as part of a specific Aβ binding domain, and G16, a 16-mer peptide with a sequence that spans strands G and H of TTR, was synthesized and tested. Although both TTR and G16 bound to Aβ, they differed significantly in their effect on Aβ aggregation, and G16 was less effective than TTR at protecting neurons from Aβ toxicity. G16 lacks the β-strand/loop/β-strand structure of TTR's Aβ binding domain. To enforce proper residue alignment, we transplanted the G16 sequence onto a β-hairpin template. Two peptides with 18 and 22 amino acids were synthesized using an orthogonally protected glutamic acid derivative, and an N-to-C cyclization reaction was carried out to further restrict conformational flexibility. The cyclized 22-mer (but not the noncyclized 22-mer nor the 18-mer) strongly suppressed Aβ aggregation into fibrils, and protected neurons against Aβ toxicity. The imposition of structural constraints generated a much-improved peptidomimetic of the Aβ binding epitope on TTR.
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Affiliation(s)
- Patricia Y. Cho
- Department of Chemical
and Biological Engineering, ‡School of Pharmacy, and §Biotechnology
Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Gururaj Joshi
- Department of Chemical
and Biological Engineering, ‡School of Pharmacy, and §Biotechnology
Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Melissa D. Boersma
- Department of Chemical
and Biological Engineering, ‡School of Pharmacy, and §Biotechnology
Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey A. Johnson
- Department of Chemical
and Biological Engineering, ‡School of Pharmacy, and §Biotechnology
Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Regina M. Murphy
- Department of Chemical
and Biological Engineering, ‡School of Pharmacy, and §Biotechnology
Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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19
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Vaněk V, Pícha J, Fabre B, Buděšínský M, Lepšík M, Jiráček J. The Development of a Versatile Trifunctional Scaffold for Biological Applications. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500255] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Groß A, Brox R, Damm D, Tschammer N, Schmidt B, Eichler J. Ligand selectivity of a synthetic CXCR4 mimetic peptide. Bioorg Med Chem 2015; 23:4050-5. [PMID: 25801155 DOI: 10.1016/j.bmc.2015.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/20/2015] [Accepted: 03/02/2015] [Indexed: 11/17/2022]
Abstract
The chemokine receptor CXCR4 belongs to the family of seven-transmembrane G-protein coupled receptors (GPCRs). It is activated by its natural ligand SDF-1α. In addition, CXCR4, along with CCR5, serve as coreceptors during HIV-1 entry into its target cell. Recently, we introduced a CXCR4 mimetic peptide, termed CX4-M1, which presents the three extracellular loops (ECLs) of the receptor. CX4-M1 was shown to selectively bind to gp120 of X4-tropic, that is, CXCR4 using, HIV-1, as well as to peptides that present the V3-loops of these gp120 proteins. Furthermore, CX4-M1 selectively inhibits infection of cells with X4-tropic HIV-1. We have now adapted the sequence of the ECLs presented by CX4-M1 to the recently published crystal structure of CXCR4. The binding behavior, as well as the effect on HIV-1 infection, of the resulting peptide (CX4-Mc) was very similar to CX4-M1, validating retrospectively the original design of CX4-M1. A peptide presenting the ECLs of CCR5 (CR5-M), on the other hand, did neither bind to gp120 from X4-tropic HIV-1, nor did it inhibit infection of cells with X4-tropic HIV-1. Furthermore, we could show that CX4-M1, as well as CX4-Mc, but not CR5-M, are selectively recognized by anti-CXCR4 antibodies, bind to SDF-1α, and also inhibit SDF-1α signaling, extending the scope of selective functional CXCR4 mimicry through CX4-M1.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Regine Brox
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Dominik Damm
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Nuška Tschammer
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Barbara Schmidt
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany.
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21
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Groß A, Rödel K, Kneidl B, Donhauser N, Mössl M, Lump E, Münch J, Schmidt B, Eichler J. Enhancement and induction of HIV-1 infection through an assembled peptide derived from the CD4 binding site of gp120. Chembiochem 2015; 16:446-54. [PMID: 25639621 DOI: 10.1002/cbic.201402545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 11/07/2022]
Abstract
Contact between the human immunodeficiency virus (HIV-1) and its target cell is initiated by the interaction of viral gp120 with cellular CD4. An assembled peptide (CD4bs-M) that presents the CD4 binding site of gp120 was previously shown to inhibit the gp120-CD4 interaction. Here, we demonstrate that CD4bs-M selectively enhances infection of cells with HIV-1, whereas infection with herpes simplex virus remains largely unaffected. The effects of CD4bs-M variants containing D-amino acids, or prolines at selected positions, point to the importance of side chain orientation and spatial orientation of this fragment. Furthermore, CD4bs-M was shown to assemble into amyloid-like fibrils that capture HIV-1 particles, which likely contributes to the infection-enhancing effect. Beyond infection enhancement, CD4bs-M enabled HIV-1 infection of CD4-negative cells, suggesting that binding of the peptide to gp120 facilitates interaction of gp120 with coreceptors, which might in turn enhance HIV-1 entry.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen (Germany)
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22
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Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O. Prediction and redesign of protein-protein interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:194-202. [PMID: 24878423 DOI: 10.1016/j.pbiomolbio.2014.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/02/2014] [Accepted: 05/17/2014] [Indexed: 12/14/2022]
Abstract
Understanding the molecular basis of protein function remains a central goal of biology, with the hope to elucidate the role of human genes in health and in disease, and to rationally design therapies through targeted molecular perturbations. We review here some of the computational techniques and resources available for characterizing a critical aspect of protein function - those mediated by protein-protein interactions (PPI). We describe several applications and recent successes of the Evolutionary Trace (ET) in identifying molecular events and shapes that underlie protein function and specificity in both eukaryotes and prokaryotes. ET is a part of analytical approaches based on the successes and failures of evolution that enable the rational control of PPI.
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Affiliation(s)
- Rhonald C Lua
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anbu K Adikesavan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angela D Wilkins
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
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23
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Zhang L, Zhang C, Sun Y. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: II. Inhibitor library, screening, and experimental validation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4734-4742. [PMID: 24697658 DOI: 10.1021/la4046012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Platelet adhesion on collagen mediated by integrin α2β1 has been proven important in arterial thrombus formation, leading to an exigent demand on development of potent inhibitors for the integrin α2β1-collagen binding. In the present study, a biomimetic design strategy of platelet adhesion inhibitors was established, based on the affinity binding model of integrin proposed in part I. First, a heptapeptide library containing 8000 candidates was designed to functionally mimic the binding motif of integrin α2β1. Then, each heptapeptide in the library was docked onto a collagen molecule for the assessment of its affinity, followed by a screening based on its structure similarity to the original structure in the affinity binding model. Eight candidates were then selected for further screening by molecular dynamics (MD) simulations. Thereafter, three candidates chosen from MD simulations were separately added into the physiological saline containing separated integrin and collagen, to check their abilities for blocking the integrin-collagen interaction using MD simulations. Of these three candidates, significant inhibition was observed in the presence of LWWNSYY. Finally, the binding affinity of LWWNSYY for collagen was demonstrated by isothermal titration calorimetry. Moreover, significant inhibition of platelet adhesion in the presence of LWWNSYY has been experimentally validated. This work has thus developed an effective strategy for the biomimetic design of peptide-based platelet adhesion inhibitors.
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Affiliation(s)
- Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072, People's Republic of China
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24
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Berthelmann A, Lach J, Gräwert MA, Groll M, Eichler J. VersatileC3-symmetric scaffolds and their use for covalent stabilization of the foldon trimer. Org Biomol Chem 2014; 12:2606-14. [DOI: 10.1039/c3ob42251h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Attachment of foldon monomers to a trimesic acid scaffold enhances thermal stability of the trimer, while maintaining the correct fold.
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Affiliation(s)
- Arne Berthelmann
- Department of Chemistry and Pharmacy
- University of Erlangen-Nurnberg
- 91052 Erlangen, Germany
| | - Johannes Lach
- Department of Chemistry and Pharmacy
- University of Erlangen-Nurnberg
- 91052 Erlangen, Germany
| | - Melissa A. Gräwert
- Center for Integrated Protein Science at the Department of Chemistry
- Chair of Biochemistry
- Technical University of Munich
- 85747 Munich, Germany
- European Molecular Biology Laboratory
| | - Michael Groll
- Center for Integrated Protein Science at the Department of Chemistry
- Chair of Biochemistry
- Technical University of Munich
- 85747 Munich, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy
- University of Erlangen-Nurnberg
- 91052 Erlangen, Germany
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25
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London N, Raveh B, Schueler-Furman O. Druggable protein-protein interactions--from hot spots to hot segments. Curr Opin Chem Biol 2013; 17:952-9. [PMID: 24183815 DOI: 10.1016/j.cbpa.2013.10.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 10/05/2013] [Accepted: 10/07/2013] [Indexed: 11/24/2022]
Abstract
Protein-Protein Interactions (PPIs) mediate numerous biological functions. As such, the inhibition of specific PPIs has tremendous therapeutic value. The notion that these interactions are 'undruggable' has petered out with the emergence of more and more successful examples of PPI inhibitors, expanding considerably the scope of potential drug targets. The accumulated data on successes in the inhibition of PPIs allow us to analyze the features that are required for such inhibition. Whereas it has been suggested and shown that targeting hot spots at PPI interfaces is a good strategy to achieve inhibition, in this review we focus on the notion that the most amenable interactions for inhibition are those that are mediated by a 'hot segment', a continuous epitope that contributes the majority of the binding energy. This criterion is both useful in guiding future target selection efforts, and in suggesting immediate inhibitory candidates--the dominant peptidic segment that mediates the targeted interaction.
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Affiliation(s)
- Nir London
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
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26
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Groß A, Möbius K, Haußner C, Donhauser N, Schmidt B, Eichler J. Mimicking Protein-Protein Interactions through Peptide-Peptide Interactions: HIV-1 gp120 and CXCR4. Front Immunol 2013; 4:257. [PMID: 24027570 PMCID: PMC3760305 DOI: 10.3389/fimmu.2013.00257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/13/2013] [Indexed: 01/21/2023] Open
Abstract
We have recently designed a soluble synthetic peptide that functionally mimics the HIV-1 coreceptor CXCR4, which is a chemokine receptor that belongs to the family of seven-transmembrane GPCRs. This CXCR4 mimetic peptide, termed CX4-M1, presents the three extracellular loops (ECLs) of the receptor. In binding assays involving recombinant proteins, as well as in cellular infection assays, CX4-M1 was found to selectively recognize gp120 from HIV-1 strains that use CXCR4 for cell entry (X4 tropic HIV-1). Furthermore, anti-HIV-1 antibodies modulate this interaction in a molecular mechanism related to that of their impact on the gp120-CXCR4 interaction. We could now show that the selectivity of CX4-M1 pertains not only to gp120 from X4 tropic HIV-1, but also to synthetic peptides presenting the V3 loops of these gp120 proteins. The V3 loop is thought to be an essential part of the coreceptor binding site of gp120 that contacts the second ECL of the coreceptor. We were able to experimentally confirm this notion in binding assays using substitution analogs of CX4-M1 and the V3 loop peptides, respectively, as well as in cellular infection assays. These results indicate that interactions of the HIV-1 Env with coreceptors can be mimicked by synthetic peptides, which may be useful to explore these interactions at the molecular level in more detail.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg , Erlangen , Germany
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27
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Alge DL, Anseth KS. Thiol‐X Reactions in Tissue Engineering. THIOL‐X CHEMISTRIES IN POLYMER AND MATERIALS SCIENCE 2013. [DOI: 10.1039/9781849736961-00165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Thiol‐based click reactions have played a key role in the synthesis of biomaterial scaffolds for regenerative medicine applications. Of particular importance has been their use in creating cell‐laden hydrogel matrices for both fundamental and translational applications. Thiol‐X reactions are often exploited in biological applications as they allow for the facile incorporation of biofunctional components, which has led to many key advancements for the field of tissue engineering. In this chapter, we summarize the important considerations for cytocompatible macromolecular monomer design and subsequent cellular encapsulation in hydrogel formulations. Briefly, we review the main thiol‐X reactions that have been used to synthesize hydrogel cell scaffold systems; provide a generalized protocol for the preparation of cell‐laden hydrogels; present highlights that demonstrate specific advantages of thiol‐X reactions and advances in their application in regenerative medicine research; and conclude with a prospectus on future directions for the field in using thiol‐X chemistries to engineer more advanced hydrogel materials.
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Affiliation(s)
- Daniel L. Alge
- Department of Chemical and Biological Engineering University of Colorado, Boulder, CO 80303‐1904 USA
| | - Kristi S. Anseth
- Department of Chemical and Biological Engineering University of Colorado, Boulder, CO 80303‐1904 USA
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28
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Kastritis PL, Bonvin AMJJ. On the binding affinity of macromolecular interactions: daring to ask why proteins interact. J R Soc Interface 2012; 10:20120835. [PMID: 23235262 PMCID: PMC3565702 DOI: 10.1098/rsif.2012.0835] [Citation(s) in RCA: 276] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Interactions between proteins are orchestrated in a precise and time-dependent manner, underlying cellular function. The binding affinity, defined as the strength of these interactions, is translated into physico-chemical terms in the dissociation constant (Kd), the latter being an experimental measure that determines whether an interaction will be formed in solution or not. Predicting binding affinity from structural models has been a matter of active research for more than 40 years because of its fundamental role in drug development. However, all available approaches are incapable of predicting the binding affinity of protein–protein complexes from coordinates alone. Here, we examine both theoretical and experimental limitations that complicate the derivation of structure–affinity relationships. Most work so far has concentrated on binary interactions. Systems of increased complexity are far from being understood. The main physico-chemical measure that relates to binding affinity is the buried surface area, but it does not hold for flexible complexes. For the latter, there must be a significant entropic contribution that will have to be approximated in the future. We foresee that any theoretical modelling of these interactions will have to follow an integrative approach considering the biology, chemistry and physics that underlie protein–protein recognition.
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Affiliation(s)
- Panagiotis L Kastritis
- Bijvoet Center for Biomolecular Research, Faculty of Science, Chemistry, Utrecht University, , Padualaan 8, Utrecht, The Netherlands
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29
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Meier J, Kassler K, Sticht H, Eichler J. Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120. Beilstein J Org Chem 2012; 8:1858-66. [PMID: 23209523 PMCID: PMC3511023 DOI: 10.3762/bjoc.8.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 09/24/2012] [Indexed: 01/31/2023] Open
Abstract
Based on the structure of the HIV-1 glycoprotein gp120 in complex with its cellular receptor CD4, we have designed and synthesized peptides that mimic the binding site of CD4 for gp120. The ability of these peptides to bind to gp120 can be strongly enhanced by increasing their conformational stability through cyclization, as evidenced by binding assays, as well as through molecular-dynamics simulations of peptide–gp120 complexes. The specificity of the peptide–gp120 interaction was demonstrated by using peptide variants, in which key residues for the interaction with gp120 were replaced by alanine or D-amino acids.
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Affiliation(s)
- Julia Meier
- Department of Chemistry and Pharmacy, Universität Erlangen-Nürnberg, Schuhstrasse 19, 91052 Erlangen, Germany
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Bonancía P, Vigara L, Galindo F, Luis SV, Jiménez MC, Miranda MA. Triplet excited state behavior of naphthalene-based pseudopeptides in the presence of energy donors. J Phys Chem B 2012; 116:9957-62. [PMID: 22860895 DOI: 10.1021/jp304883u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, the triplet state behavior of naphthalene-based pseudopeptides with amide-based macrocyclic or lateral chain substructures has been investigated in the presence of benzophenone and/or biphenyl, as suitable energy-donating chromophores. Their behavior has been compared with that of 1,4-dimethylnaphthalene as model compound. In all the cases, the triplet-triplet absorption of naphthalene is detected by transient absorption spectroscopy, upon selective excitation of benzophenone at 355 nm. The kinetics of formation and decay of this species is markedly slower in the pseudopeptides, due to retardation of triplet-triplet energy transfer and exciplex formation. Finally, the delayed fluorescence detected in the model naphthalene is absent in the pseudopeptides. The concept can, in principle, be exploited for the study of excited-state interactions in supramolecular systems.
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Affiliation(s)
- Paula Bonancía
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politécnica de Valencia, Camino de Vera s/n, 46071 Valencia, Spain
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Grimme D, González-ruiz D, Gohlke* H. Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00319] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Möbius K, Dürr R, Haußner C, Dietrich U, Eichler J. A Functionally Selective Synthetic Mimic of the HIV‐1 Co‐receptor CXCR4. Chemistry 2012; 18:8292-5. [DOI: 10.1002/chem.201200111] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 03/15/2012] [Indexed: 01/21/2023]
Affiliation(s)
- Kalle Möbius
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
| | - Ralf Dürr
- Georg‐Speyer‐Haus—Institute of Biomedical Research, Paul‐Ehrlich‐Str. 42–44, 60596 Frankfurt (Germany)
| | - Christina Haußner
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
| | - Ursula Dietrich
- Georg‐Speyer‐Haus—Institute of Biomedical Research, Paul‐Ehrlich‐Str. 42–44, 60596 Frankfurt (Germany)
| | - Jutta Eichler
- Department Chemistry and Pharmacy, Universität Erlangen‐Nürnberg, Schuhstrasse 19, 91052 Erlangen (Germany), Fax: (+49) 9131‐8522587
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Vishwanatha TM, Narendra N, Chattopadhyay B, Mukherjee M, Sureshbabu VV. Synthesis of Selenoxo Peptides and Oligoselenoxo Peptides Employing LiAlHSeH. J Org Chem 2012; 77:2689-702. [DOI: 10.1021/jo2024703] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- T. M. Vishwanatha
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
| | - N. Narendra
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
| | - Basab Chattopadhyay
- Department
of Solid State Physics, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata 700032, India
| | - Monika Mukherjee
- Department
of Solid State Physics, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata 700032, India
| | - Vommina V. Sureshbabu
- Peptide Research Laboratory,
Department of Studies in Chemistry, Central College Campus, Bangalore University, Dr. B. R. Ambedkar Veedhi, Bangalore
560001, India
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Abstract
Protein-protein interactions (PPIs) govern all aspects of cell function and, as such, are a major target for research and therapeutic intervention. A major rate-limiting step in PPI research is the expression and purification of full-length proteins. The use of peptides to study PPIs significantly facilitates the structural and biophysical characterization of PPIs as well as the effort to develop drugs to control PPIs. Here we describe examples for the use of peptides to study PPI and some of the important experimental methods that are used in the field. Peptides have proved to be excellent tools to study PPIs and have been contributing both for understanding mechanisms of PPIs as well as for drug design for PPI modulation.
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Faham A, Altin JG. Ag-bearing liposomes engrafted with peptides that interact with CD11c/CD18 induce potent Ag-specific and antitumor immunity. Int J Cancer 2011; 129:1391-403. [PMID: 21128234 DOI: 10.1002/ijc.25810] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 11/03/2010] [Indexed: 01/01/2023]
Abstract
Dendritic cells (DCs) play key role in eliciting antigen (Ag)-specific immune responses, and crucial to this is the uptake of Ag via surface receptors including the heterodimeric integrin CD11c/CD18. Here we report that CD11c/CD18-interacting peptides can be used as targeting moieties to deliver liposomal Ag to antigen presenting cells (APCs) and elicit Ag-specific and antitumor immunity. Two peptides of sequence related to human ICAM-4 and previously reported to bind CD11c/CD18, and a 12-mer cyclic peptide previously identified by phage display to bind CD11c/CD18, were produced synthetically, and tested for their ability to target liposomal Ag. The three peptides were designed to contain a shorter spacer to reduce steric hindrance, and a His-tag to enable engraftment onto liposomes incorporated with chelator lipid. Our results show that the three peptides, denoted as p17, p18 and p30, promote strong binding of liposomes to CD11c(+) and CD11b(+) cells in vitro and in vivo. Vaccination of mice with Ag-bearing liposomes engrafted with the peptides, particularly p18 and p30, induced Ag-specific T cell priming and antibody production. Importantly, the vaccination of C57BL/6 mice with syngeneic B16-OVA-derived plasma membrane vesicles (PMVs) engrafted with p18 and p30 peptide showed dramatic antitumor responses, inhibiting tumor growth/metastasis in both the lung and subcutaneous tumor models, with a high proportion of the mice apparently being "cured" of their tumors. The engraftment of p18 and p30 peptides onto liposomes and PMVs, thus provides an effective means to target Ags to DCs in vivo, for the development of effective cancer vaccines and immunotherapies.
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Affiliation(s)
- Abdus Faham
- Division of Biomedical Science and Biochemistry, Research School of Biology, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia
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Robinson JA. Protein epitope mimetics as anti-infectives. Curr Opin Chem Biol 2011; 15:379-86. [PMID: 21419690 DOI: 10.1016/j.cbpa.2011.02.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/17/2011] [Indexed: 01/09/2023]
Abstract
There is growing interest in the design of synthetic molecules that mimic the structures and functions of epitopes found on the surface of peptides and proteins. Epitope mimetics can provide valuable tools to probe complex biological processes, as well as interesting leads for drug and vaccine discovery. One application of epitope mimetics is reviewed here, focusing on mimetics of the cationic antimicrobial peptides that form part of the innate immune response to microbial and viral infection in many organisms. Mimetics of these naturally occurring peptides and proteins may be useful to explore mechanisms of antimicrobial and immunomodulatory action, and as a potential source of new antibiotics to address one of the most pressing current threats to human health.
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Affiliation(s)
- John A Robinson
- Chemistry Department, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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van de Wijngaart DJ, Dubbink HJ, Molier M, de Vos C, Jenster G, Trapman J. Inhibition of androgen receptor functions by gelsolin FxxFF peptide delivered by transfection, cell-penetrating peptides, and lentiviral infection. Prostate 2011; 71:241-53. [PMID: 20690138 DOI: 10.1002/pros.21238] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Prostate cancer (PC) growth is dependent on the androgen-androgen receptor (AR) axis. Because current androgen ablation therapies of PC lead to resistance, novel approaches to block AR activity are urgently needed. METHODS We inhibited AR function beyond the level of hormone binding by blockade of the coactivator groove in the ligand-binding domain (LBD) using a high-affinity gelsolin FxxFF peptide. Following peptide selection, the effect of the gelsolin FxxFF peptide on AR functions was determined in Hep3B cells that were transiently transfected with pM-peptide expression vectors or were incubated with synthetic gelsolin FxxFF peptide coupled to the TAT cell-penetrating peptide. Lentiviruses expressing the gelsolin FxxFF peptide were used to study endogenous AR target gene expression in LNCaP cells. RESULTS pM-Gelsolin FxxFF efficiently interfered with AR N/C interaction and specifically inhibited AR-regulated reporter gene activity. The peptide did not inhibit progesterone receptor (PR) and glucocorticoid receptor (GR) activity, nor constitutively active gene promoters. The peptide also specifically blocked in vitro interactions of AR LBD with peptides. Like the gelsolin FxxFF peptide expressed by an expression vector, synthetic TAT-gelsolin FxxFF peptide efficiently blocked AR N/C interaction and inhibited full-length AR-regulated reporter gene activity. It hardly affected PR and GR activity, but the effect on constitutively active promoters was variable. Lentiviral gelsolin FxxFF peptide inhibited expression of KLK2 and NDRG1, but hardly affected PSA and TMPRSS2. CONCLUSIONS Our results show that the AR coactivator groove may function as a target to overcome therapeutic failure that arises during current androgen ablation therapies.
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Guarracino DA, Bullock BN, Arora PS. Mini review: protein-protein interactions in transcription: a fertile ground for helix mimetics. Biopolymers 2011; 95:1-7. [PMID: 20882600 DOI: 10.1002/bip.21546] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Designed ligands that inhibit protein-protein interactions involved in gene expression are valuable as reagents for genomics research and as leads for drug discovery efforts. Selective modulation of protein-protein interactions has proven to be a daunting task for synthetic ligands; however, the last decade has seen significant advances in inhibitor design, especially for helical protein interfaces. This review discusses examples of transcriptional complexes targeted by designer helices.
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Hayouka Z, Hurevich M, Levin A, Benyamini H, Iosub A, Maes M, Shalev DE, Loyter A, Gilon C, Friedler A. Cyclic peptide inhibitors of HIV-1 integrase derived from the LEDGF/p75 protein. Bioorg Med Chem 2010; 18:8388-95. [DOI: 10.1016/j.bmc.2010.09.046] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/17/2010] [Accepted: 09/18/2010] [Indexed: 01/29/2023]
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Mooney JT, Fredericks D, Hearn MTW. Use of phage display methods to identify heptapeptide sequences for use as affinity purification 'tags' with novel chelating ligands in immobilized metal ion affinity chromatography. J Chromatogr A 2010; 1218:92-9. [PMID: 21159343 DOI: 10.1016/j.chroma.2010.10.113] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/22/2010] [Accepted: 10/26/2010] [Indexed: 01/30/2023]
Abstract
This study describes the screening of a peptide phage display library for amino acid sequences that bind with different affinities to a novel class of chelating ligands complexed with Ni²+ ions. These chelating ligands are based on the 1,4,7-triazacyclononane (TACN) structure and have been chosen to allow enhanced efficiency in protein capture and decreased propensity for metal ion leakage in the immobilized metal ion affinity chromatographic (IMAC) purification of recombinant proteins. Utilising high stringency screening conditions, various peptide sequences containing multiple histidine, tryptophan, and/or tyrosine residues were identified amongst the different phage peptide sequences isolated. The structures, and particularly the conserved locations of these key amino acid residues within the selected heptapeptides, form a basis to design specific peptide tags for use with these novel TACN ligands as a new mode of IMAC purification of recombinant proteins.
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Affiliation(s)
- Jane T Mooney
- ARC Special Research Centre for Green Chemistry, Building75, Monash University, Clayton, Victoria 3800, Australia
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41
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Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 2010; 78:2029-40. [PMID: 20455260 DOI: 10.1002/prot.22716] [Citation(s) in RCA: 313] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A wide range of regulatory processes in the cell are mediated by flexible peptides that fold upon binding to globular proteins. Computational efforts to model these interactions are hindered by the large number of rotatable bonds in flexible peptides relative to typical ligand molecules, and the fact that different peptides assume different backbone conformations within the same binding site. In this study, we present Rosetta FlexPepDock, a novel tool for refining coarse peptide-protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark that is based on a large nonredundant dataset of 89 peptide-protein interactions. Importantly, side chains of known binding motifs are modeled particularly well, typically with atomic accuracy. In addition, our protocol has improved modeling quality for the important application of cross docking to PDZ domains. We anticipate that the ability to create high resolution models for a wide range of peptide-protein complexes will have significant impact on structure-based functional characterization, controlled manipulation of peptide interactions, and on peptide-based drug design.
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Affiliation(s)
- Barak Raveh
- Department of Microbiology and Molecular Genetics, Insitute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University, Jerusalem, 91120 Israel
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Xu Z, DiCesare JC, Baures PW. Parallel synthesis of an oligomeric imidazole-4,5-dicarboxamide library. ACTA ACUST UNITED AC 2010; 12:248-54. [PMID: 20170086 DOI: 10.1021/cc1000105] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A library of oligomeric compounds was synthesized based on the imidazole-4,5-dicarboxylic acid scaffold along with amino acid esters and chiral diamines derived from amino acids. The final compounds incorporate nonpolar amino acids (Leu, Phe, Trp), polar amino acids (Ser, Asp, Arg), and neutral amino acids (Gly, Ala), and were designed to be useful in screening for inhibitors of protein-protein interactions. Many of the protected and deprotected oligomers show evidence of conformational isomers persistent at room temperature in aqueous solution. A total of 317 final oligomers, out of 441 targeted compounds, were obtained in high analytical purity and of sufficient quantity to submit them for high-throughput screening as part of the NIH Roadmap.
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Affiliation(s)
- Zhigang Xu
- Department of Chemistry and Biochemistry, The University of Tulsa, Tulsa, Oklahoma 74104, USA
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Laman AG, Shepelyakovskaya AO, Boziev KM, Savinov GV, Brovko FA, Nesmeyanov VA. A method for the preparation of adjuvant peptide mimetics of GMDP with the use of monoclonal antibodies and combinatorial libraries of peptides in the format of phage display. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:170-7. [DOI: 10.1134/s1068162010020032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Conconi MT, Ghezzo F, Dettin M, Urbani L, Grandi C, Guidolin D, Nico B, Di Bello C, Ribatti D, Parnigotto PP. Effects on in vitro and in vivo angiogenesis induced by small peptides carrying adhesion sequences. J Pept Sci 2010; 16:349-57. [DOI: 10.1002/psc.1251] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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45
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Wéber E, Hetényi A, Váczi B, Szolnoki É, Fajka-Boja R, Tubak V, Monostori É, Martinek TA. Galectin-1-Asialofetuin Interaction Is Inhibited by Peptides Containing the Tyr-Xxx-Tyr Motif Acting on the Glycoprotein. Chembiochem 2009; 11:228-34. [DOI: 10.1002/cbic.200900502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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46
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Rubinstein M, Niv MY. Peptidic modulators of protein-protein interactions: progress and challenges in computational design. Biopolymers 2009; 91:505-13. [PMID: 19226619 DOI: 10.1002/bip.21164] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
With the decline in productivity of drug-development efforts, novel approaches to rational drug design are being introduced and developed. Naturally occurring and synthetic peptides are emerging as novel promising compounds that can specifically and efficiently modulate signaling pathways in vitro and in vivo. We describe sequence-based approaches that use peptides to mimic proteins in order to inhibit the interaction of the mimicked protein with its partners. We then discuss a structure-based approach, in which protein-peptide complex structures are used to rationally design and optimize peptidic inhibitors. We survey flexible peptide docking techniques and discuss current challenges and future directions in the rational design of peptidic inhibitors.
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Affiliation(s)
- Mor Rubinstein
- The Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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47
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Kapoor S, Panda D. Targeting FtsZ for antibacterial therapy: a promising avenue. Expert Opin Ther Targets 2009; 13:1037-51. [DOI: 10.1517/14728220903173257] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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48
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Salom-Roig XJ, Martínez J, Burguete MI, Galindo F, Luis SV, Miranda MA, Morant-Miñana MC, Pérez-Prieto J. Chiral synthetic pseudopeptidic derivatives as triplet excited state quenchers. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.06.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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49
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Rossi D, Amadio M, Carnevale Baraglia A, Azzolina O, Ratti A, Govoni S, Pascale A, Collina S. Discovery of Small Peptides Derived from Embryonic Lethal Abnormal Vision Proteins Structure Showing RNA-Stabilizing Properties. J Med Chem 2009; 52:5017-9. [DOI: 10.1021/jm900741e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Daniela Rossi
- Department of Pharmaceutical Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy
| | - Marialaura Amadio
- Department of Experimental and Applied Pharmacology, University of Pavia, Viale Taramelli 14, I-27100 Pavia, Italy
| | - Anna Carnevale Baraglia
- Department of Pharmaceutical Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy
| | - Ornella Azzolina
- Department of Pharmaceutical Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy
| | - Antonia Ratti
- Department of Neurological Sciences, “Dino Ferrari” Centre, University of Milan Medical School, IRCCS Istituto Auxologico Italiano, Via Zucchi 18, I-20095 Cusano, Milan, Italy
| | - Stefano Govoni
- Department of Experimental and Applied Pharmacology, University of Pavia, Viale Taramelli 14, I-27100 Pavia, Italy
| | - Alessia Pascale
- Department of Experimental and Applied Pharmacology, University of Pavia, Viale Taramelli 14, I-27100 Pavia, Italy
| | - Simona Collina
- Department of Pharmaceutical Chemistry, University of Pavia, Viale Taramelli 12, I-27100 Pavia, Italy
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