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Ellenbroek BD, Kahler JP, Evers SR, Pomplun SJ. Synthetic Peptides: Promising Modalities for the Targeting of Disease-Related Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202401704. [PMID: 38456368 DOI: 10.1002/anie.202401704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
DNA and RNA play pivotal roles in life processes by storing and transferring genetic information, modulating gene expression, and contributing to essential cellular machinery such as ribosomes. Dysregulation and mutations in nucleic acid-related processes are implicated in numerous diseases. Despite the critical impact on health of nucleic acid mutations or dysregulation, therapeutic compounds addressing these biomolecules remain limited. Peptides have emerged as a promising class of molecules for biomedical research, offering potential solutions for challenging drug targets. This review focuses on the use of synthetic peptides to target disease-related nucleic acids. We discuss examples of peptides targeting double-stranded DNA, including the clinical candidate Omomyc, and compounds designed for regulatory G-quadruplexes. Further, we provide insights into both library-based screenings and the rational design of peptides to target regulatory human RNA scaffolds and viral RNAs, emphasizing the potential of peptides in addressing nucleic acid-related diseases.
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Affiliation(s)
| | | | - Sophie R Evers
- Leiden University, 2333 CC, Leiden, The Netherlands
- Present address, Department of Chemistry, University of Zurich, Wintherthurerstrasse 190, 8057, Zurich, Switzerland
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2
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McLoughlin NM, Albers MA, Collado Camps E, Paulus J, Ran YA, Neubacher S, Hennig S, Brock R, Grossmann TN. Environment-Responsive Peptide Dimers Bind and Stabilize Double-Stranded RNA. Angew Chem Int Ed Engl 2023; 62:e202308028. [PMID: 37603459 DOI: 10.1002/anie.202308028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023]
Abstract
Double-stranded RNAs (dsRNA) possess immense potential for biomedical applications. However, their therapeutic utility is limited by low stability and poor cellular uptake. Different strategies have been explored to enhance the stability of dsRNA, including the incorporation of modified nucleotides, and the use of diverse carrier systems. Nevertheless, these have not resulted in a broadly applicable approach thereby preventing the wide-spread application of dsRNA for therapeutic purposes. Herein, we report the design of dimeric stapled peptides based on the RNA-binding protein TAV2b. These dimers are obtained via disulfide formation and mimic the natural TAV2b assembly. They bind and stabilize dsRNA in the presence of serum, protecting it from degradation. In addition, peptide binding also promotes cellular uptake of dsRNA. Importantly, peptide dimers monomerize under reducing conditions which results in a loss of RNA binding. These findings highlight the potential of peptide-based RNA binders for the stabilization and protection of dsRNA, representing an appealing strategy towards the environment-triggered release of RNA. This can broaden the applicability of dsRNA, such as short interfering RNAs (siRNA), for therapeutic applications.
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Affiliation(s)
- Niall M McLoughlin
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Marvin A Albers
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Estel Collado Camps
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Jannik Paulus
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Youri A Ran
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Saskia Neubacher
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Incircular B.V., De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roland Brock
- Department of Medical BioSciences, Radboud University, Nijmegen Medical Center, 6525 GA, Nijmegen, The Netherlands
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, 293, Bahrain
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
- Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
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3
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Nimmagadda A, Shi Y, Cai J. γ-AApeptides as a New Strategy for Therapeutic Development. Curr Med Chem 2019; 26:2313-2329. [PMID: 29110596 DOI: 10.2174/0929867324666171107095913] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/11/2016] [Accepted: 01/16/2017] [Indexed: 12/30/2022]
Abstract
A new class of peptidomimetics termed as "γ-AApeptides" was recently developed by our group. Similar to other peptidomimetics, γ-AApeptides are resistant to proteolytic degradation, and possess limitless potential to introduce chemically diverse functional groups. γ-AApeptides have shown great promise in biomedical applications. In this article, we will review a few examples of γ-AApeptides with biological potential. Certain γ-AApeptides can permeate cell membranes and therefore they can be used as potential drug carrier. γ-AApeptides can also bind to HIV RNA with high specificity and affinity, suggesting their potential application as anti-HIV agents. Moreover, they can mimic host-defense peptides and display potent and broad-spectrum activity towards a range of drug-resistant bacterial pathogens. They are also potential anti-cancer agents. For instance, they have shown great promise in targeted imaging of tumor in mouse model, and they are also capable of disrupting p53/DNA interactions, and thus antagonize STAT3 signaling pathway. Recently, from combinatorial screening, γ-AApeptides are identified to inhibit Aβ peptide aggregation, and thus they can be developed into potential anti- Alzheimer's disease agent.
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Affiliation(s)
- Alekhya Nimmagadda
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, United States
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4
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Abstract
RNA structures play a pivotal role in many biological processes and the progression of human disease, making them an attractive target for therapeutic development. Often RNA structures operate through the formation of complexes with RNA-binding proteins, however, much like protein-protein interactions, RNA-protein interactions span large surface areas and often lack traditional druggable properties, making it challenging to target them with small molecules. Peptides provide much greater surface areas and therefore greater potential for forming specific and high affinity interactions with RNA. In this chapter, we discuss our approach for engineering peptides that bind to structured RNAs by highlighting methods and design strategies from previous successful projects aimed at inhibiting the HIV Tat-TAR interaction and the biogenesis of oncogenic microRNAs.
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Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, United States.
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5
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Bolarinwa O, Cai J. Developments with investigating descriptors for antimicrobial AApeptides and their derivatives. Expert Opin Drug Discov 2018; 13:727-739. [PMID: 29933702 DOI: 10.1080/17460441.2018.1487950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
INTRODUCTION The development of multidrug-resistant strains of bacteria resulting from prolonged treatment with conventional antibiotics has necessitated the need for continuous research for better antibiotic strategies. One of these alternatives is evolutionary antimicrobial peptides also known as host-defense peptides (HDPs). HDPs are an integral part of the innate defense system in multicellular eukaryotes. Although HDPs can largely circumvent the persistent problem of antibiotic resistance due to their bacteriolytic membrane mechanism, they have some drawbacks including a low activity profile and protease instability. AApeptides have recently been introduced as a new class of peptidomimetics with resistance to proteolysis, improved activity profile, and limitless possibilities for structural diversity. Furthermore, they have shown excellent antimicrobial activity. Areas covered: This review updates the reader on the latest developments of antimicrobial AApeptides, the various derivatizations, and their development for antimicrobial applications. The most recent findings on the heterogeneous γ-AA backbone are also outlined. Expert opinion: AApeptides have found diverse applications in antimicrobial studies. AApeptides are believed to exhibit bactericidal properties by imitating the membranolytic action of HDPs. They have shown broad-spectrum antimicrobial activity and are active against medicinally relevant drug-resistant pathogens. AApeptides and their derivatives could gain therapeutic relevance in the design and development of antibiotic agents.
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Affiliation(s)
- Olapeju Bolarinwa
- a Department of Chemistry , University of South Florida , Tampa , FL , USA
| | - Jianfeng Cai
- a Department of Chemistry , University of South Florida , Tampa , FL , USA
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6
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Molchanova N, Hansen PR, Franzyk H. Advances in Development of Antimicrobial Peptidomimetics as Potential Drugs. Molecules 2017; 22:E1430. [PMID: 28850098 PMCID: PMC6151827 DOI: 10.3390/molecules22091430] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/19/2023] Open
Abstract
The rapid emergence of multidrug-resistant pathogens has evolved into a global health problem as current treatment options are failing for infections caused by pan-resistant bacteria. Hence, novel antibiotics are in high demand, and for this reason antimicrobial peptides (AMPs) have attracted considerable interest, since they often show broad-spectrum activity, fast killing and high cell selectivity. However, the therapeutic potential of natural AMPs is limited by their short plasma half-life. Antimicrobial peptidomimetics mimic the structure and biological activity of AMPs, but display extended stability in the presence of biological matrices. In the present review, focus is on the developments reported in the last decade with respect to their design, synthesis, antimicrobial activity, cytotoxic side effects as well as their potential applications as anti-infective agents. Specifically, only peptidomimetics with a modular structure of residues connected via amide linkages will be discussed. These comprise the classes of α-peptoids (N-alkylated glycine oligomers), β-peptoids (N-alkylated β-alanine oligomers), β³-peptides, α/β³-peptides, α-peptide/β-peptoid hybrids, α/γ N-acylated N-aminoethylpeptides (AApeptides), and oligoacyllysines (OAKs). Such peptidomimetics are of particular interest due to their potent antimicrobial activity, versatile design, and convenient optimization via assembly by standard solid-phase procedures.
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Affiliation(s)
- Natalia Molchanova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
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Xu D, Jiang L, DeRidder L, Elmore B, Bukhari M, Wei Q, Samways DSK, Dong H. Membrane activity of a supramolecular peptide-based chemotherapeutic enhancer. MOLECULAR BIOSYSTEMS 2017; 12:2695-9. [PMID: 27397555 DOI: 10.1039/c6mb00369a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Self-assembly of de novo designed multidomain peptides (MDPs) resulted in functional membrane-active supramolecular nanofibers. The membrane activity was analyzed through fluorescence membrane localization and patch-clamp electrophysiology yielding important information that can be used for the development of a new type of supramolecular peptide-based chemotherapeutic enhancer.
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Affiliation(s)
- Dawei Xu
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Linhai Jiang
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Louis DeRidder
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Brendan Elmore
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
| | - Maurish Bukhari
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | - Qiang Wei
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, USA.
| | | | - He Dong
- Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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8
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Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G. A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing. ACS Chem Biol 2017; 12:1611-1620. [PMID: 28437065 DOI: 10.1021/acschembio.7b00180] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) help orchestrate cellular growth and survival through post-transcriptional mechanisms. The dysregulation of miRNA biogenesis can lead to cellular growth defects and chemotherapeutic resistance and plays a direct role in the development of many chronic diseases. Among these RNAs, miR-21 is consistently overexpressed in most human cancers, leading to the down-regulation of key tumor-suppressing and pro-apoptotic factors, suggesting that inhibition of miR-21 biogenesis could reverse these negative effects. However, targeted inhibition of miR-21 using small molecules has had limited success. To overcome difficulties in targeting RNA secondary structure with small molecules, we developed a class of cyclic β-hairpin peptidomimetics which bind to RNA stem-loop structures, such as miRNA precursors, with potent affinity and specificity. We screened an existing cyclic peptide library and discovered a lead structure which binds to pre-miR21 with KD = 200 nM and prefers it over other pre-miRNAs. The NMR structure of the complex shows that the peptide recognizes the Dicer cleavage site and alters processing of the precursor to the mature miRNA in vitro and in cultured cells. The structure provides a rationale for the peptide binding activity and clear guidance for further improvements in affinity and targeting.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Matthew J. Walker
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Yu Chen
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
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9
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Kaur P, Li Y, Cai J, Song L. Selective Membrane Disruption Mechanism of an Antibacterial γ-AApeptide Defined by EPR Spectroscopy. Biophys J 2017; 110:1789-1799. [PMID: 27119639 DOI: 10.1016/j.bpj.2016.02.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/14/2016] [Accepted: 02/19/2016] [Indexed: 12/11/2022] Open
Abstract
γ-AApeptides are a new class of antibacterial peptidomimetics that are not prone to antibiotic resistance and are highly resistant to protease degradation. It is not clear how γ-AApeptides interact with bacterial membranes and alter lipid assembly, but such information is essential to understanding their antimicrobial activities and guiding future design of more potent and specific antimicrobial agents. Using electron paramagnetic resonance techniques, we characterized the membrane interaction and destabilizing mechanism of a lipo-cyclic-γ-AApeptide (AA1), which has broad-spectrum antibacterial activities. The analyses revealed that AA1 binding increases the membrane permeability of POPC/POPG liposomes, which mimic negatively charged bacterial membranes. AA1 binding also inhibits membrane fluidity and reduces solvent accessibility around the lipid headgroup region. Moreover, AA1 interacts strongly with POPC/POPG liposomes, inducing significant lipid lateral-ordering and membrane thinning. In contrast, minimal membrane property changes were observed upon AA1 binding for liposomes mimicking mammalian cell membranes, which consist of neutral lipids and cholesterol. Our findings suggest that AA1 interacts and disrupts bacterial membranes through a carpet-like mechanism. The results showed that the intrinsic features of γ-AApeptides are important for their ability to disrupt bacterial membranes selectively, the implications of which extend to developing new antibacterial biomaterials.
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Affiliation(s)
- Pavanjeet Kaur
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida
| | - Yaqiong Li
- Department of Chemistry, University of South Florida, Tampa, Florida
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida.
| | - Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida.
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10
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Sang P, Shi Y, Teng P, Cao A, Xu H, Li Q, Cai J. Antimicrobial AApeptides. Curr Top Med Chem 2017; 17:1266-1279. [PMID: 27758686 DOI: 10.2174/1568026616666161018145945] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 05/10/2016] [Accepted: 05/18/2016] [Indexed: 12/26/2022]
Abstract
Antibiotic resistance is one of the biggest public concerns in the 21st century. Host-defense peptides (HDPs) can potentially mitigate the problem through bacterial membrane disruption; however, they suffer from moderate activity and low stability. We recently developed a new class of peptidomimetics termed "AApeptides". This class of peptidomimetics can mimic the mechanism of action of HDPs, and effectively arrest the growth of multidrug resistant Gram-positive and Gram-negative bacteria. As they are built on unnatural backbone, they are resistant to proteolytic degradation. In this review, we summarize the development of this class of antimicrobial peptidomimetics, and discuss the future perspective on how they can move forward on combating antibiotic resistance.
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Affiliation(s)
- Peng Sang
- Department of Chemistry, University of South Florida, Tampa, FL, 33260, United States
| | - Yan Shi
- Department of Chemistry, University of South Florida, Tampa, FL, 33260, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, Tampa, FL, 33260, United States
| | - Annie Cao
- Department of Chemistry, University of South Florida, Tampa, FL, 33260, United States
| | - Hai Xu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, HN 410083, China
| | - Qi Li
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, United States
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11
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Bolarinwa O, Nimmagadda A, Su M, Cai J. Structure and Function of AApeptides. Biochemistry 2017; 56:445-457. [PMID: 28029249 DOI: 10.1021/acs.biochem.6b01132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The intrinsic drawbacks encountered in bioactive peptides in chemical biology and biomedical sciences have diverted research efforts to the development of sequence-specific peptidomimetics that are capable of mimicking the structure and function of peptides and proteins. Modifications in the backbone and/or the side chain of peptides have been explored to develop biomimetic molecular probes or drug leads for biologically important targets. To expand the family of oligomeric peptidomimetics to facilitate their further application, we recently developed a new class of peptidomimetics, AApeptides based on a chiral peptide nucleic acid backbone. AApeptides are resistant to proteolytic degradation and amenable to enormous chemical diversification. Moreover, they could mimic the primary structure of peptides and also fold into discrete secondary structure such as helices and turn-like structures. Furthermore, they have started to show promise in applications in material and biomedical sciences. Herein, we highlight the structural design and some function of AApeptides and present our perspective on their future development.
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Affiliation(s)
- Olapeju Bolarinwa
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Alekhya Nimmagadda
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Ma Su
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
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12
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Abstract
Host-defense peptides (HDPs) are promising next generation of antibiotic agents, as they have the potential to circumvent emerging drug resistance, due to their mechanism of bacterial killing through disruption of their membranes. Nonetheless, HDPs have intrinsic drawbacks such as low-to-moderate activity, susceptibility to enzymatic degradation. In the past few years, we developed a new class of peptidomimetics named 'γ-AApeptides', which have superior resistance to proteolysis and a variety of diversification via straightforward synthesis. Our recent studies suggested that γ-AApeptides can mimic the bactericidal mechanism of HDPs and show potent and broad-spectrum activity against both Gram-positive and Gram-negative multidrug-resistant bacteria. In this review, we summarize our current studies of antimicrobial γ-AApeptides and discuss their potential future development as antimicrobial peptidomimetics.
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13
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Abstract
Sequence-specific peptidomimetics are molecules that mimic the structure and function of peptides and proteins. With new backbones and molecular frameworks, peptidomimetics are of considerable interest in addressing challenges encountered in chemical biology and biomedical sciences. Based on the γ-PNA backbone, a new class of peptidomimetics - "γ-AApeptides" were recently developed. Both linear and cyclic γ-AApeptides can be synthesized with high efficiency. Compared with α-peptides, γ-AApeptides are resistant to enzymatic degradation, and amendable to diversification with a variety of chemical groups. Moreover, they could mimic primary and secondary structure, as well as the function of peptides, and show promise in biological applications, such as the development of new agents combating bacteria, cancer, and Alzheimer's disease. A few research outcomes of γ-AApeptides are highlighted in this Concept article, and a future perspective is also proposed.
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Affiliation(s)
- Peng Teng
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Yan Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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14
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Shi Y, Teng P, Sang P, She F, Wei L, Cai J. γ-AApeptides: Design, Structure, and Applications. Acc Chem Res 2016; 49:428-41. [PMID: 26900964 DOI: 10.1021/acs.accounts.5b00492] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The development of sequence-specific peptidomimetics has led to a variety of fascinating discoveries in chemical biology. Many peptidomimetics can mimic primary, secondary, and even tertiary structure of peptides and proteins, and because of their unnatural backbones, they also possess significantly enhanced resistance to enzymatic hydrolysis, improved bioavailability, and chemodiversity. It is known that peptide nucleic acids (PNAs) are peptidic sequences developed for the mimicry of nucleic acids; however, their unique backbone as the molecular scaffold of peptidomimetics to mimic structure and function of bioactive peptides has not been investigated systematically. As such, we recently developed a new class of peptidomimetics, "γ-AApeptides", based on the chiral γ-PNA backbone. They are termed γ-AApeptides because they are the oligomers of γ-substituted-N-acylated-N-aminoethyl amino acids. Similar to other classes of peptidomimetics, γ-AApeptides are also resistant to proteolytic degradation and possess the potential to enhance chemodiversity. Moreover, in our scientific journey on the exploration of this class of peptidomimetics, we have discovered some intriguing structures and functions of γ-AApeptides. In this Account, we summarize the current development and application of γ-AApeptides with biological potential. Briefly, both linear and cyclic (either through head-to-tail or head-to-side-chain cyclization) γ-AApeptides with diverse functional groups can be synthesized easily on the solid phase using the synthetic protocol we developed. γ-AApeptides could mimic the primary structure of peptides, as they project the same number of side chains as peptides of the same lengths. For instance, they could mimic the Tat peptide to permeate cell membranes and bind to HIV RNA with high specificity and affinity. Certain γ-AApeptides show similar activity to the RGD peptide and target integrin specifically on the cell surface. γ-AApeptides with function akin to fMLF peptides are also identified. More importantly, we found that γ-AApeptides can fold into discrete secondary structures, such as helical and β-turn-like structures. Therefore, they could be rationally designed for a range of biological applications. For instance, γ-AApeptides can mimic host-defense peptides and display potent and broad-spectrum activity toward a panel of drug-resistant bacterial pathogens. Meanwhile, because of their stability against proteolysis and their chemodiversity, γ-AApeptides are also amenable for combinatorial screening. We demonstrate that, through combinatorial selection, certain γ-AApeptides are identified to inhibit Aβ40 peptide aggregation, suggesting their potential use as a molecular probe to intervene in Alzheimer's disease. In addition, a few γ-AApeptides identified from the γ-AApeptide library have been shown to bind to the DNA-binding domain of STAT3 and antagonize STAT3/DNA interactions. Our studies suggest that, with further studies and exploration on both structures and functions, γ-AApeptides may emerge to be a new class of peptidomimetics that play an important role in chemical biology and biomedical sciences.
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Affiliation(s)
- Yan Shi
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Teng
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Peng Sang
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Fengyu She
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Lulu Wei
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202
East Fowler Ave, Tampa, Florida 33620, United States
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15
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Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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16
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Rzuczek SG, Southern MR, Disney MD. Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy. ACS Chem Biol 2015; 10:2706-15. [PMID: 26414664 DOI: 10.1021/acschembio.5b00430] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There are many RNA targets in the transcriptome to which small molecule chemical probes and lead therapeutics are desired. However, identifying compounds that bind and modulate RNA function in cellulo is difficult. Although rational design approaches have been developed, they are still in their infancies and leave many RNAs "undruggable". In an effort to develop a small molecule library that is biased for binding RNA, we computationally identified "drug-like" compounds from screening collections that have favorable properties for binding RNA and for suitability as lead drugs. As proof-of-concept, this collection was screened for binding to and modulating the cellular dysfunction of the expanded repeating RNA (r(CUG)(exp)) that causes myotonic dystrophy type 1. Hit compounds bind the target in cellulo, as determined by the target identification approach Competitive Chemical Cross-Linking and Isolation by Pull-down (C-ChemCLIP), and selectively improve several disease-associated defects. The best compounds identified from our 320-member library are more potent in cellulo than compounds identified by high-throughput screening (HTS) campaigns against this RNA. Furthermore, the compound collection has a higher hit rate (9% compared to 0.01-3%), and the bioactive compounds identified are not charged; thus, RNA can be "drugged" with compounds that have favorable pharmacological properties. Finally, this RNA-focused small molecule library may serve as a useful starting point to identify lead "drug-like" chemical probes that affect the biological (dys)function of other RNA targets by direct target engagement.
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Affiliation(s)
- Suzanne G. Rzuczek
- Department
of Chemistry and ‡Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Mark R. Southern
- Department
of Chemistry and ‡Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department
of Chemistry and ‡Translational Research Institute, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #3A1, Jupiter, Florida 33458, United States
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17
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Wu H, Jiang J, Xu H, Li Q, Cai J. RGD mimetics γ-AApeptides and methods of use (US 20,140,004,039 A1): a patent evaluation. Expert Opin Ther Pat 2015; 26:131-7. [PMID: 26560186 DOI: 10.1517/13543776.2016.1111337] [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] [Indexed: 11/05/2022]
Abstract
The patent (US 20140004039 A1) claims Arg-Gly-Asp (RGD) mimetics based on a new type of peptidomimetics - γ-AApeptides - which display high binding affinity and specificity to integrin αvβ3. Integrin αvβ3 is one of the most important proteins involved in tumor angiogenesis and metastasis of solid tumors. It binds tightly to the tripeptide RGD, a prominent recognition motif found in extracellular matrix proteins. As αvβ3 is frequently upregulated during tumor angiogenesis, molecules mimicking the RGD recognition motif may target αvβ3 specifically and therefore can be used for cancer prevention or targeted diagnosis. Indeed, several positron emission tomography tracers targeting αvβ3 are currently under clinical investigation. γ-AApeptides as a new class of peptidomimetics show enhanced stability against proteolytic degradation and are amendable for derivatization due to their enormous chemodiversity. γ-AApeptide-based RGD mimetics, including linear, cyclic and multimeric γ-AApeptides, display comparable binding affinity and specificity to integrin αvβ3. These RGD mimetics can be synthesized easily on the solid phase and have been shown to be excellent positron emission tomography tracers by targeting glioblastoma tumor on the mouse model. As γ-AApeptide-based peptidomimetics are more stable than RGD peptides, they could be novel agents for the diagnostics and treatment of various cancers.
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Affiliation(s)
- Haifan Wu
- a Department of Pharmaceutical Chemistry , University of California , San Francisco, San Francisco , CA 94158 , USA.,b Department of Chemistry , University of South Florida , Tampa , FL 33620 , USA
| | - Jinzhi Jiang
- c College of Chemistry and Chemical Engineering , Central South University , Changsha , HN 410083 , P. R. China
| | - Hai Xu
- c College of Chemistry and Chemical Engineering , Central South University , Changsha , HN 410083 , P. R. China
| | - Qi Li
- d Department of Medical Oncology, Shuguang Hospital , Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Jianfeng Cai
- b Department of Chemistry , University of South Florida , Tampa , FL 33620 , USA
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18
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Wu H, Qiao Q, Teng P, Hu Y, Antoniadis D, Zuo X, Cai J. New Class of Heterogeneous Helical Peptidomimetics. Org Lett 2015; 17:3524-7. [PMID: 26153619 DOI: 10.1021/acs.orglett.5b01608] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new class of unnatural heterogeneous foldamers is reported to contain alternative α-amino acid and sulfono-γ-AA amino acid residues in a 1:1 repeat pattern. Two-dimensional NMR data show that two 1:1 α/sulfono-γ-AA peptides with diverse side chains form analogous right-handed helical structures in solution. The effects of sequence length, side chain, N-capping, and temperature on folding propensity were further investigated using circular dichroism and small-angle X-ray scattering.
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Affiliation(s)
- Haifan Wu
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Qiao Qiao
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Peng Teng
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Yaogang Hu
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Dimitrios Antoniadis
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Xiaobing Zuo
- ‡X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jianfeng Cai
- †Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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19
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Wu H, She F, Gao W, Prince A, Li Y, Wei L, Mercer A, Wojtas L, Ma S, Cai J. The synthesis of head-to-tail cyclic sulfono-γ-AApeptides. Org Biomol Chem 2015; 13:672-6. [DOI: 10.1039/c4ob02232g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Head-to-tail cyclic sulfono-γ-AApeptides.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Fengyu She
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Wenyang Gao
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Austin Prince
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Yaqiong Li
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Lulu Wei
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Allison Mercer
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Lukasz Wojtas
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Shengqian Ma
- Department of Chemistry
- University of South Florida
- Tampa
- USA
| | - Jianfeng Cai
- Department of Chemistry
- University of South Florida
- Tampa
- USA
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20
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Wu H, Qiao Q, Hu Y, Teng P, Gao W, Zuo X, Wojtas L, Larsen RW, Ma S, Cai J. Sulfono-γ-AApeptides as a new class of nonnatural helical foldamer. Chemistry 2014; 21:2501-7. [PMID: 25504756 DOI: 10.1002/chem.201406112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Indexed: 11/06/2022]
Abstract
Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono-γ-AApeptide foldamers of varying lengths. The crystal structure of the sulfono-γ-AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono-γ-AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two-dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right-handed helical structure. Optical analysis using circular dichroism further supports well- defined helical conformation of sulfono-γ-AApeptides in solution containing as few as five building blocks. Future development of sulfono-γ-AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620 (USA)
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21
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Hu Y, Cheng N, Wu H, Kang S, Ye RD, Cai J. Design, synthesis and characterization of fMLF-mimicking AApeptides. Chembiochem 2014; 15:2420-6. [PMID: 25224835 DOI: 10.1002/cbic.201402396] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Indexed: 01/12/2023]
Abstract
The tripeptide N-formyl-Met-Leu-Phe (fMLF) is a potent neutrophil chemoattractant and the reference agonist for the G protein-coupled N-formylpeptide receptor (FPR). As it plays a very important role in host defense and inflammation, there has been considerable interest in the development of fMLF analogues in the hope of identifying potential therapeutic agents. Herein we report the design, synthesis, and evaluation of AApeptides that mimic the structure and function of fMLF. The lead AApeptides induced calcium mobilization and mitogen-activated protein kinase (MAPK) signal transduction pathways in FPR-transfected rat basophilic leukemic (RBL) cells. More intriguingly, at high concentrations, certain AApeptides were more effective than fMLF in the induction of calcium mobilization. Their agonistic activity is further supported by their ability to stimulate chemotaxis and the production of superoxide in HL-60 cells. Similarly to fMLF, these AApeptides are much more selective towards FPR1 than FPR2. These results suggest that the fMLF-mimicking AApeptides might emerge as a new class of therapeutic agents that target FPRs.
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Affiliation(s)
- Yaogang Hu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620 (USA)
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22
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Méndez-Samperio P. Peptidomimetics as a new generation of antimicrobial agents: current progress. Infect Drug Resist 2014; 7:229-37. [PMID: 25210467 PMCID: PMC4155802 DOI: 10.2147/idr.s49229] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance is an increasing public health concern around the world. Rapid increase in the emergence of multidrug-resistant bacteria has been the target of extensive research efforts to develop a novel class of antibiotics. Antimicrobial peptides (AMPs) are small cationic amphiphilic peptides, which play an important role in the defense against bacterial infections through disruption of their membranes. They have been regarded as a potential source of future antibiotics, owing to a remarkable set of advantageous properties such as broad-spectrum activity, and they do not readily induce drug-resistance. However, AMPs have some intrinsic drawbacks, such as susceptibility to enzymatic degradation, toxicity, and high production cost. Currently, a new class of AMPs termed “peptidomimetics” have been developed, which can mimic the bactericidal mechanism of AMPs, while being stable to enzymatic degradation and displaying potent activity against multidrug-resistant bacteria. This review will focus on current findings of antimicrobial peptidomimetics. The potential future directions in the development of more potent analogs of peptidomimetics as a new generation of antimicrobial agents are also presented.
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Affiliation(s)
- Patricia Méndez-Samperio
- Department of Immunology, National School of Biological Sciences, National Polytechnic Institute, Mexico City, Mexico
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23
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Li Y, Smith C, Wu H, Teng P, Shi Y, Padhee S, Jones T, Nguyen AM, Cao C, Yin H, Cai J. Short antimicrobial lipo-α/γ-AA hybrid peptides. Chembiochem 2014; 15:2275-80. [PMID: 25169879 DOI: 10.1002/cbic.201402264] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Indexed: 12/22/2022]
Abstract
The last two decades have seen the rise of antimicrobial peptides (AMPs) to combat emerging antibiotic resistance. Herein we report the solid-phase synthesis of short lipidated α/γ-AA hybrid peptides. This family of lipo-chimeric peptidomimetics displays potent and broad-spectrum antimicrobial activity against a range of multi-drug resistant Gram-positive and Gram-negative bacteria. These lipo-α/γ-AA hybrid peptides also demonstrate high biological specificity, with no hemolytic activity towards red blood cells. Fluorescence microscopy suggests that these lipo-α/γ-AA chimeric peptides can mimic the mode of action of AMPs and kill bacterial pathogens via membrane disintegration. As the composition of these chimeric peptides is simple, therapeutic development could be economically feasible and amenable for a variety of antimicrobial applications.
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Affiliation(s)
- Yaqiong Li
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620 (USA)
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24
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Rapid Access to Multiple Classes of Peptidomimetics from Common γ-AApeptide Building Blocks. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301841] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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25
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Wu H, Li Y, Bai G, Niu Y, Qiao Q, Tipton JD, Cao C, Cai J. γ-AApeptide-based small-molecule ligands that inhibit Aβ aggregation. Chem Commun (Camb) 2013; 50:5206-8. [PMID: 24158240 DOI: 10.1039/c3cc46685j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the design, synthesis, characterization and evaluation of a novel class of γ-AApeptide one-bead-one-compound (OBOC) library, from which a small γ-AApeptide was identified to effectively prevent and disassemble Aβ aggregation.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA.
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26
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Niu Y, Wu H, Li Y, Hu Y, Padhee S, Li Q, Cao C, Cai J. AApeptides as a new class of antimicrobial agents. Org Biomol Chem 2013; 11:4283-90. [PMID: 23722277 DOI: 10.1039/c3ob40444g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antibiotic resistance is an increasing public health concern around the world, and is recognized as one of the greatest threats facing humankind in the 21(st) century. Natural antimicrobial peptides (AMPs) are small cationic amphiphilic peptides found in virtually all living organisms, and play a key role in the defense against bacterial infections. Compared with conventional antibiotics, which target specific metabolic processes, AMPs are able to adopt globally amphipathic conformations, and kill bacteria through disruption of their membranes. As such, AMPs do not readily induce drug-resistance. However, AMPs are associated with intrinsic drawbacks such as low-to-moderate activity, susceptibility to enzymatic degradation, and inconvenience for optimization. Recently, we have developed a new class of peptidomimetics termed "AApeptides". Such peptide mimics are highly resistant to protease degradation and are straightforward for chemical diversification and development. Our current studies show that AApeptides with globally amphipathic structures can mimic the bactericidal mechanism of AMPs, and display potent and broad-spectrum activity against both Gram-positive and -negative multi-drug-resistant bacteria. In this review, we summarize our current findings of antimicrobial AApeptides, and discuss potential future directions on the development of more potent and specific analogues.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA
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27
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Abstract
Antimicrobial peptides (AMPs) hold promise to circumvent the emergence of drug resistance occurring in the treatment of bacteria using many conventional antibiotics. Antimicrobial peptidomimetics, which mimic bactericidal mechanisms of AMPs, may overcome the disadvantages of AMPs and become the new generation of antibiotic therapeutics. In this review, some recent examples in the development of antimicrobial peptidomimetics are highlighted. The potential of antimicrobial agents has been demonstrated for therapeutic uses. Meanwhile, perspectives on their further development and applications are also presented.
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28
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Abstract
The creation and development of nonnatural peptidomimetics has become an area of increasing significance in bioorganic and chemical biology. A wide range of new peptide mimics with novel structures and functions are urgently needed to be explored in order to identify potential drug candidates and targeted probes, and to study protein functions. AApeptides are a new class of peptide mimics based on chiral PNA backbone. They are resistant to proteolytic degradation and have limitless potential for diversification. They have been found to have a wide variety of biological applications including cellular translocation, disruption of protein-protein interactions, formation of nanostructures, antimicrobial activity, etc. The synthesis of AApeptides is modular and straightforward. In this chapter, methods for the synthesis of AApeptides (including different subclasses) are described.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, Tampa, FL, USA
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29
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Niu Y, Wu H, Huang R, Qiao Q, Costanza F, Wang XS, Hu Y, Amin MN, Nguyen AM, Zhang J, Haller E, Ma S, Li X, Cai J. Nanorods Formed from a New Class of Peptidomimetics. Macromolecules 2012. [DOI: 10.1021/ma3015992] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Rongfu Huang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Qiao Qiao
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Frankie Costanza
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Xi-Sen Wang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Yaogang Hu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Mohamad Nassir Amin
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Anh-My Nguyen
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - James Zhang
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Edward Haller
- Department of Integrative Biology, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Shengqian Ma
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Xiao Li
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave., Tampa,
Florida 33620, United States
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30
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Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA. J Nucleic Acids 2012; 2012:971581. [PMID: 22957210 PMCID: PMC3432390 DOI: 10.1155/2012/971581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
Folded RNA molecules have recently emerged as critical regulatory elements in biological pathways, serving not just as carriers of genetic information but also as key components in enzymatic assemblies. In particular, the transactivation response element (TAR) of the HIV genome regulates transcriptional elongation by interacting specifically with the Tat protein, initiating the recruitment of the elongation complex. Preventing this interaction from occurring in vivo halts HIV replication, thus making RNA-binding molecules an intriguing pharmaceutical target. Using α-amino acids as starting materials, we have designed and synthesized a new class of polyamino-amido oligomers, called PAAs, specifically for binding to folded RNA structures. The PAA monomers were readily incorporated into a 125-member combinatorial library of PAA trimers. In order to rapidly assess RNA binding, a quantum dot-based fluorescent screen was developed to visualize RNA binding on-resin. The binding affinities of hits were quantified using a terbium footprinting assay, allowing us to identify a ligand (SFF) with low micromolar affinity (kd = 14 μM) for TAR RNA. The work presented herein represents the development of a flexible scaffold that can be easily synthesized, screened, and subsequently modified to provide ligands specific for binding to folded RNAs.
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31
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Yang Y, Niu Y, Hong H, Wu H, Zhang Y, Engle JW, Barnhart TE, Cai J, Cai W. Radiolabeled γ-AApeptides: a new class of tracers for positron emission tomography. Chem Commun (Camb) 2012; 48:7850-2. [PMID: 22785080 DOI: 10.1039/c2cc33620k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A γ-AApeptide-based tracer for positron emission tomography imaging of integrin α(v)β(3) is reported. Despite its shorter sequence and linear nature, this tracer had comparable integrin α(v)β(3) binding affinity to the cyclic arginine-glycine-aspartic acid peptide but significantly higher resistance to enzymatic degradation and better stability.
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Affiliation(s)
- Yunan Yang
- Department of Radiology, University of Wisconsin - Madison, WI 53705, USA
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32
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Wu H, Amin MN, Niu Y, Qiao Q, Harfouch N, Nimer A, Cai J. Solid-phase synthesis of γ-AApeptides using a submonomeric approach. Org Lett 2012; 14:3446-9. [PMID: 22731678 DOI: 10.1021/ol301406a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solid-phase synthesis of γ-AApeptides using a novel submonomeric approach that utilizes an allyl protection is reported. The strategy successfully circumvents the necessity of preparing γ-AApeptide building blocks in order to prepare γ-AApeptide sequences. This method will maximize the potential of developing chemically diverse γ-AApeptide libraries and thereby facilitate the biological applications of γ-AApeptides in the future.
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Affiliation(s)
- Haifan Wu
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, USA
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33
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Niu Y, Padhee S, Wu H, Bai G, Qiao Q, Hu Y, Harrington L, Burda WN, Shaw LN, Cao C, Cai J. Lipo-γ-AApeptides as a new class of potent and broad-spectrum antimicrobial agents. J Med Chem 2012; 55:4003-9. [PMID: 22475244 DOI: 10.1021/jm300274p] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is increasing demand to develop antimicrobial peptides (AMPs) as next generation antibiotic agents, as they have the potential to circumvent emerging drug resistance against conventional antibiotic treatments. Non-natural antimicrobial peptidomimetics are an ideal example of this, as they have significant potency and in vivo stability. Here we report for the first time the design of lipidated γ-AApeptides as antimicrobial agents. These lipo-γ-AApeptides show potent broad-spectrum activities against fungi and a series of Gram-positive and Gram-negative bacteria, including clinically relevant pathogens that are resistant to most antibiotics. We have analyzed their structure-function relationship and antimicrobial mechanisms using membrane depolarization and fluorescent microscopy assays. Introduction of unsaturated lipid chain significantly decreases hemolytic activity and thereby increases the selectivity. Furthermore, a representative lipo-γ-AApeptide did not induce drug resistance in S. aureus, even after 17 rounds of passaging. These results suggest that the lipo-γ-AApeptides have bactericidal mechanisms analogous to those of AMPs and have strong potential as a new class of novel antibiotic therapeutics.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, CHE 205, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, USA
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34
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Niu Y, Bai G, Wu H, Wang RE, Qiao Q, Padhee S, Buzzeo R, Cao C, Cai J. Cellular translocation of a γ-AApeptide mimetic of Tat peptide. Mol Pharm 2012; 9:1529-34. [PMID: 22413929 DOI: 10.1021/mp300070w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-penetrating peptides including the trans-activating transcriptional activator (Tat) from HIV-1 have been used as carriers for intracellular delivery of a myriad of cargoes including drugs, molecular probes, DNAs and nanoparticles. Utilizing fluorescence flow cytometry and confocal fluorescence microscopy, we demonstrate that a γ-AApeptide mimetic of Tat (48-57) can cross the cell membranes and enter the cytoplasm and nucleus of cells, with efficiency comparable to or better than that of Tat peptide (48-57). Deletion of the four side chains of the γ-AApeptide attenuates translocation capability. We also establish that the γ-AApeptide is even less toxic than the Tat peptide against mammalian cells. In addition to their low toxicity, γ-AApeptides are resistant to protease degradation, which may prove to be advantageous over α-peptides for further development of molecular transporters for intracellular delivery.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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35
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Wu H, Niu Y, Padhee S, Wang RE, Li Y, Qiao Q, Bai G, Cao C, Cai J. Design and synthesis of unprecedented cyclic γ-AApeptides for antimicrobial development. Chem Sci 2012. [DOI: 10.1039/c2sc20428b] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Niu Y, Padhee S, Wu H, Bai G, Harrington L, Burda WN, Shaw LN, Cao C, Cai J. Identification of γ-AApeptides with potent and broad-spectrum antimicrobial activity. Chem Commun (Camb) 2011; 47:12197-12199. [PMID: 21963627 DOI: 10.1039/c1cc14476f] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the identification of a new class of antimicrobial peptidomimetics-γ-AApeptides with potent and broad-spectrum activity, including clinically-relevant strains that are unresponsive to most antibiotics. They are also not prone to select for drug-resistance.
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Affiliation(s)
- Youhong Niu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA. ; ; Tel: +1-813-974-9506
| | - Shruti Padhee
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA. ; ; Tel: +1-813-974-9506
| | - Haifan Wu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA. ; ; Tel: +1-813-974-9506
| | - Ge Bai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA. ; ; Tel: +1-813-974-9506
| | - Lacey Harrington
- Department of Cell Biology, Microbiology and Molecular Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Whittney N Burda
- Department of Cell Biology, Microbiology and Molecular Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, 4202 E. Fowler Ave, Tampa, FL 33620, USA
| | - Chuanhai Cao
- Department of Molecular Pharmacology and Physiology, USF-Health Byrd Alzheimer's Institute, 4001 E. Fletcher Ave, Tampa, FL 33613, USA
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL 33620, USA. ; ; Tel: +1-813-974-9506
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