bims-cepepe 2023-09-03 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2023–09–03
ten papers selected by
Henry Lamb, Queensland University of Technology

Development of a Selective Peptide κ-Opioid Receptor Antagonist by Late-Stage Functionalization with Cysteine Staples.
Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination.
Proteolytically Stable Diaza-Peptide Foldamers Mimic Helical Hot Spots of Protein-Protein Interactions and Act as Natural Chaperones.
MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions.
Rational peptide design for targeting cancer cell invasion.
A combination of a cell penetrating peptide and a protein translation inhibitor kills metastatic breast cancer cells.
Structural and functional characterisation of Tst2, a novel TRPV1 inhibitory peptide from the Australian sea anemone Telmatactis stephensoni.
Designing Potent Anticancer Peptides by Aurein 1.2 Key Residues Mutation and Catenate Cell-Penetrating Peptide.
From oncolytic peptides to oncolytic polymers: A new paradigm for oncotherapy.
Targeting drug-tolerant cells: A promising strategy for overcoming acquired drug resistance in cancer cells.

J Med Chem. 2023 Aug 26.

Development of a Selective Peptide κ-Opioid Receptor Antagonist by Late-Stage Functionalization with Cysteine Staples.

Edin Muratspahić, Andrew M White, Cosmin I Ciotu, Nadine Hochrainer, Nataša Tomašević, Johannes Koehbach, Richard J Lewis, Mariana Spetea, Michael J M Fischer, David J Craik, Christian W Gruber.

The κ-opioid receptor (KOR) is an attractive target for the development of novel drugs. KOR agonists are potentially safer pain medications, whereas KOR antagonists are promising drug candidates for the treatment of neuropsychiatric disorders. Hitherto, the vast majority of selective drug leads that have been developed for KOR are small molecules. In this study, novel peptide probes were designed by using an endogenous dynorphin A1-13 sequence as a template for peptide stapling via late-stage cysteine functionalization. Leveraging this strategy, we developed a stable and potent KOR antagonist, CSD-CH2(1,8)-NH2, with approximately 1000-fold improved selectivity for KOR over μ- and δ-opioid receptors. Its potent competitive KOR antagonism was verified in KOR-expressing cells, peripheral dorsal root ganglion neurons, and using the tail-flick and rotarod tests in mice. This work highlights the value of cysteine stapling to develop selective peptide probes to modulate central KOR function, as innovative peptide drug candidates for the treatment of KOR-related illnesses.

DOI: https://doi.org/10.1021/acs.jmedchem.3c00426
Int J Biol Macromol. 2023 Aug 24. pii: S0141-8130(23)03422-0. [Epub ahead of print]252 126526

Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination.

Sungwoo Choi, Seung Han Son, Min Young Kim, Insung Na, Vladimir N Uversky, Chul Geun Kim.

  Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds promise for drug development. However, experimental confirmation of the peculiarities of PPIs is challenging due to their dynamic and transient nature. As a complement to experimental technologies, multiple computational molecular docking (MD) methods have been developed to predict the structures of protein-protein complexes and their dynamics, still requiring further improvements in several issues. Here, we report an improved MD method, namely three-software docking (3SD), by employing three popular protein-peptide docking software (CABS-dock, HPEPDOCK, and HADDOCK) in combination to ensure constant quality for most targets. We validated our 3SD performance in known protein-peptide interactions (PpIs). We also enhanced MD performance in proteins having intrinsically disordered regions (IDRs) by applying the modified 3SD strategy, the three-software docking after removing random coiled IDR (3SD-RR), to the comparable crystal PpI structures. At the end, we applied 3SD-RR to the AlphaFold2-predicted receptors, yielding an efficient prediction of PpI pose with high relevance to the experimental data regardless of the presence of IDRs or the availability of receptor structures. Our study provides an improved solution to the challenges in studying PPIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery. SIGNIFICANCE STATEMENT: Protein-protein interactions (PPIs) are integral to life, and abnormal PPIs are associated with diseases such as cancer. Studying protein-peptide interactions (PpIs) is challenging due to their dynamic and transient nature. Here we developed improved docking methods (3SD and 3SD-RR) to predict the PpI poses, ensuring constant quality in most targets and also addressing issues like intrinsically disordered regions (IDRs) and artificial intelligence-predicted structures. Our study provides an improved solution to the challenges in studying PpIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery.

Keywords:  AlphaFold2; Intrinsically disordered region (IDR); Protein-peptide binding pose (PpBP); Protein-peptide docking; Protein-protein interaction (PPI)

DOI:  https://doi.org/10.1016/j.ijbiomac.2023.126526
J Med Chem. 2023 Aug 26.

Proteolytically Stable Diaza-Peptide Foldamers Mimic Helical Hot Spots of Protein-Protein Interactions and Act as Natural Chaperones.

Chenghui Shi, Julia Kaffy, Tâp Ha-Duong, Jean-François Gallard, Alain Pruvost, Aloise Mabondzo, Lidia Ciccone, Sandrine Ongeri, Nicolo Tonali.

A novel class of peptidomimetic foldamers based on diaza-peptide units are reported. Circular dichroism, attenuated total reflection -Fourier transform infrared, NMR, and molecular dynamics studies demonstrate that unlike the natural parent nonapeptide, the specific incorporation of one diaza-peptide unit at the N-terminus allows helical folding in water, which is further reinforced by the introduction of a second unit at the C-terminus. The ability of these foldamers to resist proteolysis, to mimic the small helical hot spot of transthyretin-amyloid β (Aβ) cross-interaction, and to decrease pathological Aβ aggregation demonstrates that the introduction of diaza-peptide units is a valid approach for designing mimics or inhibitors of protein-protein interaction and other therapeutic peptidomimetics. This study also reveals that small peptide foldamers can play the same role as physiological chaperone proteins and opens a new way to design inhibitors of amyloid protein aggregation, a hallmark of more than 20 serious human diseases such as Alzheimer's disease.

DOI: https://doi.org/10.1021/acs.jmedchem.3c00611
Brief Bioinform. 2023 Aug 31. pii: bbad310. [Epub ahead of print]

MpbPPI: a multi-task pre-training-based equivariant approach for the prediction of the effect of amino acid mutations on protein-protein interactions.

Yang Yue, Shu Li, Lingling Wang, Huanxiang Liu, Henry H Y Tong, Shan He.

  The accurate prediction of the effect of amino acid mutations for protein-protein interactions (PPI $\Delta \Delta G$) is a crucial task in protein engineering, as it provides insight into the relevant biological processes underpinning protein binding and provides a basis for further drug discovery. In this study, we propose MpbPPI, a novel multi-task pre-training-based geometric equivariance-preserving framework to predict PPI $\Delta \Delta G$. Pre-training on a strictly screened pre-training dataset is employed to address the scarcity of protein-protein complex structures annotated with PPI $\Delta \Delta G$ values. MpbPPI employs a multi-task pre-training technique, forcing the framework to learn comprehensive backbone and side chain geometric regulations of protein-protein complexes at different scales. After pre-training, MpbPPI can generate high-quality representations capturing the effective geometric characteristics of labeled protein-protein complexes for downstream $\Delta \Delta G$ predictions. MpbPPI serves as a scalable framework supporting different sources of mutant-type (MT) protein-protein complexes for flexible application. Experimental results on four benchmark datasets demonstrate that MpbPPI is a state-of-the-art framework for PPI $\Delta \Delta G$ predictions. The data and source code are available at https://github.com/arantir123/MpbPPI.

Keywords:  equivariant neural network; multi-task pre-training; protein binding affinity change prediction; protein engineering

DOI:  https://doi.org/10.1093/bib/bbad310
Proteins. 2023 Aug 30.

Rational peptide design for targeting cancer cell invasion.

Mohammad Mahmoudi Gomari, Seyed Shahriar Arab, Saeed Balalaie, Sorour Ramezanpour, Arshad Hosseini, Nikolay V Dokholyan, Parastoo Tarighi.

  Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion. Because of their low production cost and ease of production, peptides are valuable therapeutic molecules for inhibiting cancer cell invasion. In recent years, advances in the field of computational biology have facilitated the design of anti-cancer peptides. In our investigation, using computational biology approaches such as evolutionary analysis, residue scanning, protein-peptide interaction analysis, molecular dynamics, and free energy analysis, our team designed a peptide library with about 100 000 candidates based on A6 (acetyl-KPSSPPEE-amino) sequence which is an anti-invasion peptide. During computational studies, two of the designed peptides that give the highest scores and showed the greatest sequence similarity to A6 were entered into the experimental analysis workflow for further analysis. In experimental analysis steps, the anti-metastatic potency and other therapeutic effects of designed peptides were evaluated using MTT assay, RT-qPCR, zymography analysis, and invasion assay. Our study disclosed that the IK1 (acetyl-RPSFPPEE-amino) peptide, like A6, has great potency to inhibit the invasion of cancer cells.

Keywords:  CD44; cancer; invasion; matrix metalloproteinases; peptide design; uPA-uPAR

DOI:  https://doi.org/10.1002/prot.26580
Cell Death Discov. 2023 Aug 31. 9(1): 325

A combination of a cell penetrating peptide and a protein translation inhibitor kills metastatic breast cancer cells.

Linda Rowland, Henri-Baptiste Marjault, Ola Karmi, DeAna Grant, Lauren J Webb, Assaf Friedler, Rachel Nechushtai, Ron Elber, Ron Mittler.

Cell Penetrating Peptides (CPPs) are promising anticancer and antimicrobial drugs. We recently reported that a peptide derived from the human mitochondrial/ER membrane-anchored NEET protein, Nutrient Autophagy Factor 1 (NAF-1; NAF-144-67), selectively permeates and kills human metastatic epithelial breast cancer cells (MDA-MB-231), but not control epithelial cells. As cancer cells alter their phenotype during growth and metastasis, we tested whether NAF-144-67 would also be efficient in killing other human epithelial breast cancer cells that may have a different phenotype. Here we report that NAF-144-67 is efficient in killing BT-549, Hs 578T, MDA-MB-436, and MDA-MB-453 breast cancer cells, but that MDA-MB-157 cells are resistant to it. Upon closer examination, we found that MDA-MB-157 cells display a high content of intracellular vesicles and cellular protrusions, compared to MDA-MB-231 cells, that could protect them from NAF-144-67. Inhibiting the formation of intracellular vesicles and dynamics of cellular protrusions of MDA-MB-157 cells, using a protein translation inhibitor (the antibiotic Cycloheximide), rendered these cells highly susceptible to NAF-144-67, suggesting that under certain conditions, the killing effect of CPPs could be augmented when they are applied in combination with an antibiotic or chemotherapy agent. These findings could prove important for the treatment of metastatic cancers with CPPs and/or treatment combinations that include CPPs.

DOI: https://doi.org/10.1038/s41420-023-01627-3
Biochim Biophys Acta Proteins Proteom. 2023 Aug 26. pii: S1570-9639(23)00066-3. [Epub ahead of print] 140952

Structural and functional characterisation of Tst2, a novel TRPV1 inhibitory peptide from the Australian sea anemone Telmatactis stephensoni.

Khaled A Elnahriry, Dorothy C C Wai, Lauren M Ashwood, Muhammad Umair Naseem, Tibor G Szanto, Shaodong Guo, Gyorgy Panyi, Peter J Prentis, Raymond S Norton.

  Sea anemone venoms are complex mixtures of biologically active compounds, including disulfide-rich peptides, some of which have found applications as research tools, and others as therapeutic leads. Our recent transcriptomic and proteomic studies of the Australian sea anemone Telmatactis stephensoni identified a transcript for a peptide designated Tst2. Tst2 is a 38-residue peptide showing sequence similarity to peptide toxins known to interact with a range of ion channels (NaV, TRPV1, KV and CaV). Recombinant Tst2 (rTst2, which contains an additional Gly at the N-terminus) was produced by periplasmic expression in Escherichia coli, enabling the production of both unlabelled and uniformly 13C,15N-labelled peptide for functional assays and structural studies. The LC-MS profile of the recombinant Tst2 showed a pure peak with molecular mass 6 Da less than that of the reduced form of the peptide, indicating the successful formation of three disulfide bonds from its six cysteine residues. The solution structure of rTst2 was determined using multidimensional NMR spectroscopy and revealed that rTst2 adopts an inhibitor cystine knot (ICK) structure. rTst2 was screened using various functional assays, including patch-clamp electrophysiological and cytotoxicity assays. rTst2 was inactive against voltage-gated sodium channels (NaV) and the human voltage-gated proton (hHv1) channel. rTst2 also did not possess cytotoxic activity when assessed against Drosophila melanogaster flies. However, the recombinant peptide at 100 nM showed >50% inhibition of the transient receptor potential subfamily V member 1 (TRPV1) and slight (~10%) inhibition of transient receptor potential subfamily A member 1 (TRPA1). Tst2 is thus a novel ICK inhibitor of the TRPV1 channel.

Keywords:  Disulfide-rich peptides; ICK scaffold; NMR spectroscopy; Recombinant expression; Sea anemone; TRPV1 channel

DOI:  https://doi.org/10.1016/j.bbapap.2023.140952
Adv Pharm Bull. 2023 Jul;13(3): 583-591

Designing Potent Anticancer Peptides by Aurein 1.2 Key Residues Mutation and Catenate Cell-Penetrating Peptide.

Hamta Salarpour Garnaie, Arman Shahabi, Mohammad Hossein Geranmayeh, Abolfazel Barzegar, Ahmad Yari Khosroushahi.

   Purpose: Aurein 1.2 (Aur) peptide is known for possessing anticancer characteristics devoid of conventional therapeutics side effects. For improving Aur peptide anticancer functionality, different anticancer peptides were constructed based on Aur peptide through targeting two separate strategies, including (1) sequence-based mutations and (2) adding a cell-penetrating peptide linker.
Methods: The study was approached by designing three different analogs of Aur, including (a) Aur mutant (Aurm), (b) Aur with N-terminal polyarginine linker (R5-Aur), and (c) Aurm with R5 (R5-Aurm). Computational molecular dynamics simulations clearly showed higher structural stability of R5-Aur and R5-Aurm compared to Aur, solely. The α-helical properties of R5-Aur and R5-Aurm were protected during 500 ns simulations in water solution while no such structural conservation was seen for Aur in silico.
Results: The results of the current study highlight response to one of the main challenges of cancer therapy through selective invasion of Aur to cancer cells without significant involvement of normal cells. This issue was confirmed by different assays, including: MTT assay, flow cytometry, qPCR, and nuclei morphological observations. Furthermore, this study intensifies exploiting in silico approaches for adjusting drug delivery. The results of different assessments on designed peptides reveal an anticancer activity pattern rising from Aur toward Aurm, and R5- Aur, consecutively.
Conclusion: The designed structure of Aur shows improved anticancer activity through molecular changes which makes it suggestable for anticancer therapies.

Keywords:  Anticancer peptides; Aurein 1.2; Cancer; Cell-penetrating peptide

DOI:  https://doi.org/10.34172/apb.2023.063
Bioact Mater. 2024 Jan;31 206-230

From oncolytic peptides to oncolytic polymers: A new paradigm for oncotherapy.

Hanmeng Liu, Wei Shen, Wanguo Liu, Zexin Yang, Dengke Yin, Chunsheng Xiao.

  Traditional cancer therapy methods, especially those directed against specific intracellular targets or signaling pathways, are not powerful enough to overcome tumor heterogeneity and therapeutic resistance. Oncolytic peptides that can induce membrane lysis-mediated cancer cell death and subsequent anticancer immune responses, has provided a new paradigm for cancer therapy. However, the clinical application of oncolytic peptides is always limited by some factors such as unsatisfactory bio-distribution, poor stability, and off-target toxicity. To overcome these limitations, oncolytic polymers stand out as prospective therapeutic materials owing to their high stability, chemical versatility, and scalable production capacity, which has the potential to drive a revolution in cancer treatment. This review provides an overview of the mechanism and structure-activity relationship of oncolytic peptides. Then the oncolytic peptides-mediated combination therapy and the nano-delivery strategies for oncolytic peptides are summarized. Emphatically, the current research progress of oncolytic polymers has been highlighted. Lastly, the challenges and prospects in the development of oncolytic polymers are discussed.

Keywords:  Cancer therapy; Immunotherapy; Oncolytic peptides; Oncolytic polymers; Therapeutic resistance

DOI:  https://doi.org/10.1016/j.bioactmat.2023.08.007
MedComm (2020). 2023 Oct;4(5): e342

Targeting drug-tolerant cells: A promising strategy for overcoming acquired drug resistance in cancer cells.

Xiaohai Song, Yang Lan, Xiuli Zheng, Qianyu Zhu, Xuliang Liao, Kai Liu, Weihan Zhang, QiangBo Peng, Yunfeng Zhu, Linyong Zhao, Xiaolong Chen, Yang Shu, Kun Yang, Jiankun Hu.

  Drug resistance remains the greatest challenge in improving outcomes for cancer patients who receive chemotherapy and targeted therapy. Surmounting evidence suggests that a subpopulation of cancer cells could escape intense selective drug treatment by entering a drug-tolerant state without genetic variations. These drug-tolerant cells (DTCs) are characterized with a slow proliferation rate and a reversible phenotype. They reside in the tumor region and may serve as a reservoir for resistant phenotypes. The survival of DTCs is regulated by epigenetic modifications, transcriptional regulation, mRNA translation remodeling, metabolic changes, antiapoptosis, interactions with the tumor microenvironment, and activation of signaling pathways. Thus, targeting the regulators of DTCs opens a new avenue for the treatment of therapy-resistant tumors. In this review, we first provide an overview of common characteristics of DTCs and the regulating networks in DTCs development. We also discuss the potential therapeutic opportunities to target DTCs. Last, we discuss the current challenges and prospects of the DTC-targeting approach to overcome acquired drug resistance. Reviewing the latest developments in DTC research could be essential in discovering of methods to eliminate DTCs, which may represent a novel therapeutic strategy for preventing drug resistance in the future.

Keywords:  acquired drug resistance; drug‐tolerant cells; phenotype plasticity; translational remodeling

DOI:  https://doi.org/10.1002/mco2.342