bims-cepepe 2024-02-11 papers

bims-cepepe

Biomed News

on Cell-penetrating peptides

Issue of 2024–02–11
twenty-six papers selected by
Henry Lamb, Queensland University of Technology

Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation.
Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.
A Structure-Activity Relationship Study of SNAIL1 Peptides as Inhibitors of Lysine-Specific Demethylase 1.
Helical peptides with disordered regions for measles viruses provide new generalized insights into fusion inhibitors.
Charge of a transmembrane peptide alters its interaction with lipid membranes.
Preclinical evaluation of 68 Ga-labeled peptide CK2 for PET imaging of NRP-1 expression in vivo.
Increased interaction between connexin43 and microtubules is critical for glioblastoma stem-like cell maintenance and tumorigenicity.
Discovery of a novel potent EGFR inhibitor against EGFR activating mutations and on-target resistance in NSCLC.
The Blood-Brain Barrier: Implications for Experimental Cancer Therapeutics.
The Biology of Lipids.
Detailed investigation of the binding abilities of the heterodomain of a multiHis cyclopeptide toward Cu(II) ions.
Rational Design of Amphipathic Antimicrobial Peptides with Alternating L-/D-Amino Acids That Form Helical Structures.
Design of dual peptide-conjugated hydrogels for proliferation and differentiation of human pluripotent stem cells.
Advancing the Boundaries of Immunotherapy in Lung Adenocarcinoma with Idiopathic Pulmonary Fibrosis by a Biomimetic Proteinoid Enabling Selective Endocytosis.
Somatostatin Receptor Imaging with [18F]FET-βAG-TOCA PET/CT and [68Ga]Ga-DOTA-Peptide PET/CT in Patients with Neuroendocrine Tumors: A Prospective, Phase 2 Comparative Study.
LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer.
A virtual library of small molecules mimicking dipeptides.
Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide.
Design, synthesis and biological evaluation of novel cyclic malonamide derivatives as selective RIPK1 inhibitors.
PMIpred: a physics-informed web server for quantitative Protein-Membrane interaction prediction.
The Oncogenic Lipid Sphingosine-1-Phosphate Impedes the Phagocytosis of Tumor Cells by M1 Macrophages in Diffuse Large B Cell Lymphoma.
The Effect of Non-Overlapping Somatic Mutations in BRAF, NRAS, NF1, or CKIT on the Incidence and Outcome of Brain Metastases during Immune Checkpoint Inhibitor Therapy of Metastatic Melanoma.
Exploring the substrate stereoselectivity and catalytic mechanism of nonribosomal peptide macrocyclization in surugamides biosynthesis.
NIR-II Conjugated Electrolytes as Biomimetics of Lipid Bilayers for In Vivo Liposome Tracking.
Deep2Pep: A deep learning method in multi-label classification of bioactive peptide.
Bioactive peptides: an alternative therapeutic approach for cancer management.

J Am Chem Soc. 2024 Feb 08.

Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation.

Justin H Faris, Emel Adaligil, Nataliya Popovych, Satoshi Ono, Mifune Takahashi, Huy Nguyen, Emile Plise, Jaru Taechalertpaisarn, Hsiau-Wei Lee, Michael F T Koehler, Christian N Cunningham, R Scott Lokey.

The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.

DOI: https://doi.org/10.1021/jacs.3c10949
Int J Mol Sci. 2024 Feb 01. pii: 1798. [Epub ahead of print]25(3):

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.

Marian Vincenzi, Flavia Anna Mercurio, Marilisa Leone.

  Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).

Keywords:  PPIs; anticancer peptides; antiviral peptides; bioactive peptides; drug discovery; virtual screening

DOI:  https://doi.org/10.3390/ijms25031798
Chem Pharm Bull (Tokyo). 2024 ;72(2): 155-160

A Structure-Activity Relationship Study of SNAIL1 Peptides as Inhibitors of Lysine-Specific Demethylase 1.

Yuri Takada, Kyohei Adachi, Yuka Fujinaga, Yasunobu Yamashita, Yukihiro Itoh, Takayoshi Suzuki.

  Peptides have recently garnered attention as middle-molecular-weight drugs with the characteristics of small molecules and macromolecules. Lysine-specific demethylase 1 (LSD1) is a potential therapeutic target for lung cancer, neuroblastoma, and leukemia, and some peptide-based LSD1 inhibitors designed based on the N-terminus of SNAIL1, a member of the SNAIL/SCRATCH family of transcription factors, have been reported. The N-terminus of SNAIL1 peptide acts as a cap of the catalytic site of LSD1, inhibiting interactions with LSD1. However, the structure-activity relationship (SAR) of these inhibitors is not yet fully understood. Therefore, in the present study, we aimed to uncover the SAR and to identify novel SNAIL1 peptide-based LSD1 inhibitors. We synthesized peptide inhibitor candidates based on truncating the N-terminus of SNAIL1 or substituting its amino acid residues. In the truncation study, we found that SNAIL1 1-16 (2), which was composed of 16 residues, strongly inhibited LSD1. Furthermore, we investigated the SAR at residues-3 and -5 from the N-terminus and found that peptides 2j and 2k, in which leucine 5 of the parent peptide is substituted with unnatural amino acids, cyclohexylalanine and norleucine, respectively, strongly inhibited LSD1. This result suggests that the hydrophobic interaction between the inhibitor peptides and LSD1 affects the LSD1-inhibitory activity. We believe that this SAR information provides a basis for the development of more potent LSD1 inhibitors.

Keywords:  middle-molecular-weight peptide; peptide design; peptide-based inhibitor; unnatural amino acid

DOI:  https://doi.org/10.1248/cpb.c23-00671
iScience. 2024 Feb 16. 27(2): 108961

Helical peptides with disordered regions for measles viruses provide new generalized insights into fusion inhibitors.

Kazushige Hirata, Aoi Takahara, Satoshi Suzuki, Shumei Murakami, Kumi Kawaji, Akie Nishiyama, Mina Sasano, Mariko Shoji-Ueno, Emiko Usui, Kazutaka Murayama, Hironori Hayashi, Shinya Oishi, Eiichi N Kodama.

  Despite effective vaccines, measles virus (MeV) outbreaks occur sporadically. Therefore, developing anti-MeV agents remains important for suppressing MeV infections. We previously designed peptide-based MeV fusion inhibitors, M1 and M2, that target MeV class I fusion protein (F protein). Here, we developed a novel fusion inhibitor, MEK35, that exerts potent activity against M1/M2-resistant MeV variants. Comparing MEK35 to M1 derivatives revealed that combining disordered and helical elements was essential for overcoming M1/M2 resistance. Moreover, we propose a three-step antiviral process for peptide-based fusion inhibitors: (i) disordered peptides interact with F protein; (ii) the peptides adopt a partial helical conformation and bind to F protein through hydrophobic interactions; and (iii) subsequent interactions involving the disordered region of the peptides afford a peptide-F protein with a high-affinity peptide-F protein interaction. An M1-resistant substitution blocks the second step. These results should aid the development of novel viral fusion inhibitors targeting class I F protein.

Keywords:  Molecular biology; Virology

DOI:  https://doi.org/10.1016/j.isci.2024.108961
Colloids Surf B Biointerfaces. 2024 Jan 23. pii: S0927-7765(24)00023-7. [Epub ahead of print]235 113765

Charge of a transmembrane peptide alters its interaction with lipid membranes.

Garima C N Thakur, Arunima Uday, Marek Cebecauer, Wouter H Roos, Lukasz Cwiklik, Martin Hof, Piotr Jurkiewicz, Adéla Melcrová.

  Transmembrane (TM) proteins interact closely with the surrounding membrane lipids. Lipids in the vicinity of TM proteins were reported to have hindered mobility, which has been associated with lipids being caught up in the rough surface of the TM domains. These reports, however, neglect one important factor that largely influences the membrane behavior - electrostatics of the TM peptides that are usually positively charged at their cytosolic end. Here, we study on the example of a neutral and a positively charged WALP peptide, how the charge of a TM peptide influences the membrane. We investigate both its dynamics and mechanics by: (i) time dependent fluorescent shift in combination with classical and FRET generalized polarization to evaluate the mobility of lipids at short and long-range distance from the peptide, (ii) atomic force microscopy to observe the mechanical stability of the peptide-containing membranes, and (iii) molecular dynamics simulations to analyze the peptide-lipid interactions. We show that both TM peptides lower lipid mobility in their closest surroundings. The peptides cause lateral heterogeneity in lipid mobility, which in turn prevents free lipid rearrangement and lowers the membrane ability to seal ruptures after mechanical indentations. Introduction of a positive charge to the peptide largely enhances these effects, affecting the whole membrane. We thus highlight that unspecific peptide-lipid interactions, especially the electrostatics, should not be overlooked as they have a great impact on the mechanics and dynamics of the whole membrane.

Keywords:  AFM imaging; AFM nanoindentation; FRET-GP; Integral membrane protein; MD simulation

DOI:  https://doi.org/10.1016/j.colsurfb.2024.113765
Eur J Nucl Med Mol Imaging. 2024 Feb 06.

Preclinical evaluation of 68 Ga-labeled peptide CK2 for PET imaging of NRP-1 expression in vivo.

Qingzhu Liu, Shuyue Cai, Jiacong Ye, Quan Xie, Rongbin Liu, Ling Qiu, Jianguo Lin.

   PURPOSE: Neuropilin-1 (NRP-1) is a multifunctional protein involved in a variety of biological processes such as angiogenesis, tumorigenesis and immunomodulation. It was usually overexpressed in many cancer cell lines and correlated with poor prognosis of breast cancer. Positron emission tomography (PET) is an advanced imaging technique for detecting the function and metabolism of tumor-associated molecules in real time, dynamically, quantitatively and noninvasively. To improve the level of early diagnosis and evaluate the prognosis of breast cancer, an NRP-1 targeting peptide-based tracer [68 Ga]Ga-NOTA-PEG4-CK2 was designed to sensitively and specifically detect the NRP-1 expression in vivo via PET imaging.
METHODS: In silico modeling and microscale thermophoresis (MST) assay were carried out to design the NRP-1 targeting peptide NOTA-PEG4-CK2, and it was further radiolabeled with 68 Ga to prepare the tracer [68 Ga]Ga-NOTA-PEG4-CK2. The radiochemical yield (RCY), radiochemical purity (RCP), molar activity (Am), lipid-water partition coefficient (Log P) and stability of [68 Ga]Ga-NOTA-PEG4-CK2 were assessed. The targeting specificity of the tracer for NRP-1 was investigated by in vitro cellular uptake assay and in vivo PET imaging as well as blocking studies. The sensitivity of the tracer in monitoring the dynamic changes of NRP-1 expression induced by chemical drug was also investigated in vitro and in vivo. Ex vivo biodistribution, autoradiography, western blot, and immunofluorescence staining were also performed to study the specificity of [68 Ga]Ga-NOTA-PEG4-CK2 for NRP-1.
RESULTS: [68 Ga]Ga-NOTA-PEG4-CK2 was designed and synthesized with high RCY (> 98%), high stability (RCP > 95%) and high affinity to NRP-1 (KD = 25.39 ± 1.65 nM). In vitro cellular uptake assay showed that the tracer [68 Ga]Ga-NOTA-PEG4-CK2 can specifically bind to NRP-1 positive cancer cells MDA-MB-231 (1.04 ± 0.04% at 2 h) rather than NRP-1 negative cancer cells NCI-H1299 (0.43 ± 0.05%). In vivo PET imaging showed the maximum tumor uptake of [68 Ga]Ga-NOTA-PEG4-CK2 in MDA-MB-231 xenografts (4.16 ± 0.67%ID/mL) was significantly higher than that in NCI-H1299 xenografts (1.03 ± 0.19%ID/mL) at 10 min post injection, and the former exhibited higher tumor-to-muscle uptake ratio (5.22 ± 0.18) than the latter (1.07 ± 0.27) at 60 min post injection. MDA-MB-231 xenografts pretreated with nonradioactive precursor NOTA-PEG4-CK2 showed little tumor uptake of [68 Ga]Ga-NOTA-PEG4-CK2 (1.67 ± 0.38%ID/mL at 10 min post injection). Both cellular uptake assay and PET imaging revealed that NRP-1 expression in breast cancer MDA-MB-231 could be effectively suppressed by SB-203580 treatment and can be sensitively detected by [68 Ga]Ga-NOTA-PEG4-CK2. Ex vivo analysis also proved the high specificity and sensitivity of [68 Ga]Ga-NOTA-PEG4-CK2 for NRP-1 expression in MDA-MB-231 xenografts.
CONCLUSION: A promising NRP-1 targeting PET tracer [68 Ga]Ga-NOTA-PEG4-CK2 was successfully prepared. It showed remarkable specificity and sensitivity in monitoring the dynamic changes of NRP-1 expression. Hence, it could provide valuable information for early diagnosis of NRP-1 relevant cancers and evaluating the prognosis of cancer patients.

Keywords:  68 Ga-labeling; Breast cancer; Neuropilin-1 (NRP-1); Peptide; Positron emission tomography (PET)

DOI:  https://doi.org/10.1007/s00259-024-06632-x
bioRxiv. 2024 Jan 27. pii: 2024.01.26.576347. [Epub ahead of print]

Increased interaction between connexin43 and microtubules is critical for glioblastoma stem-like cell maintenance and tumorigenicity.

James W Smyth, Sujuan Guo, Lorie O'Rourke, Stacie Deaver, Jacob Dahlka, Elmar Nurmemmedov, Zhi Sheng, Robert G Gourdie, Samy Lamouille.

Glioblastoma (GBM) is the most common primary tumor of the central nervous system. One major challenge in GBM treatment is the resistance to chemotherapy and radiotherapy observed in subpopulations of cancer cells, including GBM stem-like cells (GSCs). These cells hold the ability to self-renew or differentiate following treatment, participating in tumor recurrence. The gap junction protein connexin43 (Cx43) has complex roles in oncogenesis and we have previously demonstrated an association between Cx43 and GBM chemotherapy resistance. Here, we report, for the first time, increased direct interaction between non-junctional Cx43 with microtubules in the cytoplasm of GSCs. We hypothesize that non-junctional Cx43/microtubule complexing is critical for GSC maintenance and survival and sought to specifically disrupt this interaction while maintaining other Cx43 functions, such as gap junction formation. Using a Cx43 mimetic peptide of the carboxyl terminal tubulin-binding domain of Cx43 (JM2), we successfully ablated Cx43 interaction with microtubules in GSCs. Importantly, administration of JM2 significantly decreased GSC survival in vitro , and limited GSC-derived tumor growth in vivo . Together, these results identify JM2 as a novel peptide drug to ablate GSCs in GBM treatment.

DOI: https://doi.org/10.1101/2024.01.26.576347
Clin Cancer Res. 2024 Feb 08.

Discovery of a novel potent EGFR inhibitor against EGFR activating mutations and on-target resistance in NSCLC.

Eun Ji Lee, Seung Yeon Oh, You Won Lee, Ju Young Kim, Min-Je Kim, Tae Ho Kim, Jii Bum Lee, Min Hee Hong, Sun Min Lim, Anke Baum, Lydia Woelflingseder, Harald Engelhardt, Mark Petronczki, Flavio Solca, Mi Ran Yun, Byoung Chul Cho.

PURPOSE: Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) serve as the standard first-line therapy for EGFR-mutated non-small-cell lung cancer (NSCLC). Despite the sustained clinical benefits achieved through optimal EGFR-TKI treatments, including the third-generation EGFR-TKI osimertinib, resistance inevitably develops. Currently, there are no targeted therapeutic options available post-progression on osimertinib. Here, we assessed the preclinical efficacy of BI-4732, a novel fourth-generation EGFR-TKI, using patient-derived preclinical models reflecting various clinical scenarios.
EXPERIMENTAL DESIGN: The antitumor activity of BI-4732 was evaluated using Ba/F3 cells and patient-derived cell/organoid/xenograft models with diverse EGFR mutations. Intracranial antitumor activity of BI-4732 was evaluated in a brain-metastasis mouse model.
RESULTS: We demonstrated the remarkable antitumor efficacy of BI-4732 as a single agent in various patient-derived models with EGFR_C797S-mediated osimertinib resistance. Moreover, BI-4732 exhibited activity comparable to osimertinib in inhibiting EGFR-activating (E19del and L858R) and T790M mutations. In a combination treatment strategy with osimertinib, BI-4732 exhibited a synergistic effect at significantly lower concentrations than those used in monotherapy. Importantly, BI-4732 displayed potent antitumor activity in an intracranial model, with low efflux at the blood-brain barrier (BBB).
CONCLUSIONS: Our findings highlight the potential of BI-4732, a selective EGFR-TKI with high BBB penetration, targeting a broad range of EGFR mutations, including C797S, warranting clinical development.

DOI: https://doi.org/10.1158/1078-0432.CCR-23-2951
Annu Rev Cancer Biol. 2023 Apr;7 265-289

The Blood-Brain Barrier: Implications for Experimental Cancer Therapeutics.

Joelle P Straehla, David A Reardon, Patrick Y Wen, Nathalie Y R Agar.

  The blood-brain barrier is critically important for the treatment of both primary and metastatic cancers of the central nervous system (CNS). Clinical outcomes for patients with primary CNS tumors are poor and have not significantly improved in decades. As treatments for patients with extracranial solid tumors improve, the incidence of CNS metastases is on the rise due to suboptimal CNS exposure of otherwise systemically active agents. Despite state-of-the art surgical care and increasingly precise radiation therapy, clinical progress is limited by the ability to deliver an effective dose of a therapeutic agent to all cancerous cells. Given the tremendous heterogeneity of CNS cancers, both across cancer subtypes and within a single tumor, and the range of diverse therapies under investigation, a nuanced examination of CNS drug exposure is needed. With a shared goal, common vocabulary, and interdisciplinary collaboration, the field is poised for renewed progress in the treatment of CNS cancers.

Keywords:  blood-brain barrier; central nervous system tumors; drug delivery; pharmacodynamics; pharmacokinetics; therapeutic development

DOI:  https://doi.org/10.1146/annurev-cancerbio-061421-040433
Cold Spring Harb Perspect Biol. 2024 Feb 05. pii: a041713. [Epub ahead of print]

The Biology of Lipids.

Robert G Parton, Kai Simons.

Lipids are the defining features of cellular membranes. They act collectively to form a variety of different structures, and understanding their complex behavior represents an early example of systems biology. A multidisciplinary approach is needed to analyse the functions of lipids in biological systems, and new work is providing fascinating insights into their roles in membrane biology, metabolism, signaling, subcellular dynamics and various disease processes.

DOI: https://doi.org/10.1101/cshperspect.a041713
J Pept Sci. 2024 Feb 05. e3568

Detailed investigation of the binding abilities of the heterodomain of a multiHis cyclopeptide toward Cu(II) ions.

Marco Bortolus, Aleksandra Kotynia, Giacomo Saielli, Paolo Ruzza, Marilena Di Valentin, Mauro Carraro, Justyna Brasuń.

  Cyclopeptides hold significant relevance in various fields of science and medicine, due to their unique structural properties and diverse biological activities. Cyclic peptides, characterized by intrinsically higher conformational order, exhibit remarkable stability and resistance to proteolytic degradation, making them attractive candidates for developing targeted drug delivery systems. The aim of this work is to elucidate the unique coordination properties of the multi-His cyclic peptide with c(HDHKHPHHKHHP) sequence (HDCP - heterodomain cyclopeptide). This peptide, indeed, is able to form homo- and hetero-dinuclear complexes in a wide pH range, being thus a good chelator for Cu(II) ions. Herein, we present the results of a combined study, involving potentiometric, spectroscopic (UV-Vis, CD, and EPR), and computational investigations, on its coordination properties. To better understand the interaction pattern with Cu(II) metal ions, two other peptides, each one bearing only one of the two binding domains of HDCP are also considered in this study: c(HDHKHPGGKGGP) = CP1, c(GKGGKPHHKHHP) = CP2, which share sequence fragments of HDCP and allow separate investigations of its coordination domains.

Keywords:  CD spectroscopy; UV-vis spectroscopy; copper ion; cyclopeptides; dinuclear complex; potentiometric titration; thermodynamic stability constant

DOI:  https://doi.org/10.1002/psc.3568
Chem Pharm Bull (Tokyo). 2024 ;72(2): 149-154

Rational Design of Amphipathic Antimicrobial Peptides with Alternating L-/D-Amino Acids That Form Helical Structures.

Motoharu Hirano, Hidetomo Yokoo, Nobumichi Ohoka, Takahito Ito, Takashi Misawa, Makoto Oba, Takao Inoue, Yosuke Demizu.

  Antimicrobial peptides (AMPs) are promising therapeutic agents against bacteria. We have previously reported an amphipathic AMP Stripe composed of cationic L-Lys and hydrophobic L-Leu/L-Ala residues, and Stripe exhibited potent antimicrobial activity against Gram-positive and Gram-negative bacteria. Gramicidin A (GA), composed of repeating sequences of L- and D-amino acids, has a unique β6.3-helix structure and exhibits broad antimicrobial activity. Inspired by the structural properties and antimicrobial activities of LD-alternating peptides such as GA, in this study, we designed Stripe derivatives with LD-alternating sequences. We found that simply alternating L- and D-amino acids in the Stripe sequence to give StripeLD caused a reduction in antimicrobial activity. In contrast, AltStripeLD, with cationic and hydrophobic amino acids rearranged to yield an amphipathic distribution when the peptide adopts a β6.3-helix, displayed higher antimicrobial activity than AltStripe. These results suggest that alternating L-/D-cationic and L-/D-hydrophobic amino acids in accordance with the helical structure of an AMP may be a useful way to improve antimicrobial activity and develop new AMP drugs.

Keywords:  LD-peptide; amphipathicity; antimicrobial peptide; α-helix; β6.3-helix

DOI:  https://doi.org/10.1248/cpb.c23-00465
Mater Today Bio. 2024 Apr;25 100969

Design of dual peptide-conjugated hydrogels for proliferation and differentiation of human pluripotent stem cells.

Tzu-Cheng Sung, Yen-Hung Chen, Ting Wang, Liu Qian, Wen-Hui Chao, Jun Liu, Jiandong Pang, Qing-Dong Ling, Henry Hsin-Chung Lee, Akon Higuchi.

  Completely synthetic cell cultivation materials for human pluripotent stem cells (hPSCs) are important for the future clinical use of hPSC-derived cells. Currently, cell culture materials conjugated with extracellular matrix (ECM)-derived peptides are being prepared using only one specific integrin-targeting peptide. We designed dual peptide-conjugated hydrogels, for which each peptide was selected from different ECM sites: the laminin β4 chain and fibronectin or vitronectin, which can target α6β1 and α2β1 or αVβ5. hPSCs cultured on dual peptide-conjugated hydrogels, especially on hydrogels conjugated with peptides obtained from the laminin β4 chain and vitronectin with a low peptide concentration of 200 μg/mL, showed high proliferation ability over the long term and differentiated into cells originating from 3 germ layers in vivo as well as a specific lineage of cardiac cells. The design of grafting peptides was also important, for which a joint segment and positive amino acids were added into the designed peptide. Because of the designed peptides on the hydrogels, only 200 μg/mL peptide solution was sufficient for grafting on the hydrogels, and the hydrogels supported hPSC cultures long-term; in contrast, in previous studies, greater than 1000 μg/mL peptide solution was needed for the grafting of peptides on cell culture materials.

Keywords:  Cardiomyocyte; Human pluripotent stem cells; Hydrogel; Integrin; Peptide; Proliferation

DOI:  https://doi.org/10.1016/j.mtbio.2024.100969
ACS Nano. 2024 Feb 06.

Advancing the Boundaries of Immunotherapy in Lung Adenocarcinoma with Idiopathic Pulmonary Fibrosis by a Biomimetic Proteinoid Enabling Selective Endocytosis.

Aimin Jiang, Xiaoqiang Zheng, Siqi Yan, Jin Yan, Yu Yao, Wangxiao He.

  The coexistence of lung adenocarcinoma (LUAD) with idiopathic pulmonary fibrosis (IPF), which has been extensively documented as a prominent risk factor for checkpoint inhibitor-related pneumonitis (CIP) in patients undergoing immunotherapy, has long been considered a restricted domain for the use of immune checkpoint inhibitors (ICIs). To overcome it, an approach was employed herein to specifically target PD-L1 within the cellular interior, surpassing the conventional focus solely on the cytomembrane, thereby facilitating the development of ICIs capable of distinguishing between LUAD cells and noncancerous cells based on their distinctive endocytic propensities. By exploiting the aurophilicity-driven self-assembly of a PD-L1 binding peptide (PDBP) and subsequently encapsulating it within erythrocyte membranes (EM), the resulting biomimetic ICIs protein EMS-PDBP exhibited extraordinary selectivity in internalizing LUAD cells, effectively targeting PD-L1 within cancer cells while hindering its membrane translocation. The EMS-PDBP treatment not only reactivated the antitumor immune response in the LUAD orthotopic allograft mouse model but also demonstrated a favorable safety profile by effectively eliminating any immune-related adverse events (irAEs). Most significantly, EMS-PDBP successfully and safely restored the antitumor immune response in a mouse model of LUAD with coexistent IPF, thus shattering the confines of ICIs immunotherapy. The reported EMS-PDBP collectively offers a potential strategy for immune reactivation to overcome the limitations of immunotherapy in LUAD coexisting with IPF.

Keywords:  biomimetic supramolecular; idiopathic pulmonary fibrosis; immune-related adverse events; immunotherapy; lung adenocarcinoma

DOI:  https://doi.org/10.1021/acsnano.3c09852
J Nucl Med. 2024 Feb 08. pii: jnumed.123.266601. [Epub ahead of print]

Somatostatin Receptor Imaging with [18F]FET-βAG-TOCA PET/CT and [68Ga]Ga-DOTA-Peptide PET/CT in Patients with Neuroendocrine Tumors: A Prospective, Phase 2 Comparative Study.

Suraiya Dubash, Tara D Barwick, Kasia Kozlowski, Andrea G Rockall, Sairah Khan, Sameer Khan, Siraj Yusuf, Angela Lamarca, Juan W Valle, Richard A Hubner, Mairéad G McNamara, Andrea Frilling, Tricia Tan, Florian Wernig, Jeannie Todd, Karim Meeran, Bhavesh Pratap, Saleem Azeem, Michael Huiban, Nicholas Keat, Jingky P Lozano-Kuehne, Eric O Aboagye, Rohini Sharma.

  There is a clinical need for 18F-labeled somatostatin analogs for the imaging of neuroendocrine tumors (NET), given the limitations of using [68Ga]Ga-DOTA-peptides, particularly with regard to widespread accessibility. We have shown that [18F]fluoroethyl-triazole-[Tyr3]-octreotate ([18F]FET-βAG-TOCA) has favorable dosimetry and biodistribution. As a step toward clinical implementation, we conducted a prospective, noninferiority study of [18F]FET-βAG-TOCA PET/CT compared with [68Ga]Ga-DOTA- peptide PET/CT in patients with NET. Methods: Forty-five patients with histologically confirmed NET, grades 1 and 2, underwent PET/CT imaging with both [18F]FET-βAG-TOCA and [68Ga]Ga-peptide performed within a 6-mo window (median, 77 d; range, 6-180 d). Whole-body PET/CT was conducted 50 min after injection of 165 MBq of [18F]FET-βAG-TOCA. Tracer uptake was evaluated by comparing SUVmax and tumor-to-background ratios at both lesion and regional levels by 2 unblinded, experienced readers. A randomized, blinded reading of both scans was also then undertaken by 3 experienced readers, and consensus was assessed at a regional level. The ability of both tracers to visualize liver metastases was also assessed. Results: A total of 285 lesions were detected on both imaging modalities. An additional 13 tumor deposits were seen in 8 patients on [18F]FET-βAG-TOCA PET/CT, and [68Ga]Ga-DOTA-peptide PET/CT detected an additional 7 lesions in 5 patients. Excellent correlation in SUVmax was observed between both tracers (r = 0.91; P < 0.001). No difference was observed between median SUVmax across regions, except in the liver, where the median tumor-to-background ratio of [18F]FET-βAG-TOCA was significantly lower than that of [68Ga]Ga-DOTA-peptide (2.5 ± 1.9 vs. 3.5 ± 2.3; P < 0.001). Conclusion: [18F]FET-βAG-TOCA was not inferior to [68Ga]Ga-DOTA-peptide in visualizing NET and may be considered in routine clinical practice given the longer half-life and availability of the cyclotron-produced fluorine radioisotope.

Keywords:  PET; [18F]FET-βAG-TOCA; [68Ga]Ga-DOTA-peptide; neuroendocrine tumors; somatostatin receptor

DOI:  https://doi.org/10.2967/jnumed.123.266601
bioRxiv. 2024 Jan 22. pii: 2024.01.17.576106. [Epub ahead of print]

LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer.

A Mandl, S Jasmine, Teg Krueger, R Kumar, I M Coleman, S L Dalrymple, L Antony, D M Rosen, Y Jing, B Hanratty, R A Patel, L Jin-Yih, J Dias, C A Celatka, A E Tapper, M Kleppe, M Kanayama, V Speranzini, Y Z Wang, J Luo, E Corey, L A Sena, R A Casero, T Lotan, B J Trock, S K Kachhap, S R Denmeade, M A Carducci, A Mattevi, M C Haffner, P S Nelson, H Y Rienhoff, J T Isaacs, W N Brennen.

Lysine-specific demethylase 1 (LSD1 or KDM1A ) has emerged as a critical mediator of tumor progression in metastatic castration-resistant prostate cancer (mCRPC). Among mCRPC subtypes, neuroendocrine prostate cancer (NEPC) is an exceptionally aggressive variant driven by lineage plasticity, an adaptive resistance mechanism to androgen receptor axis-targeted therapies. Our study shows that LSD1 expression is elevated in NEPC and associated with unfavorable clinical outcomes. Using genetic approaches, we validated the on-target effects of LSD1 inhibition across various models. We investigated the therapeutic potential of bomedemstat, an orally bioavailable, irreversible LSD1 inhibitor with low nanomolar potency. Our findings demonstrate potent antitumor activity against CRPC models, including tumor regressions in NEPC patient-derived xenografts. Mechanistically, our study uncovers that LSD1 inhibition suppresses the neuronal transcriptional program by downregulating ASCL1 through disrupting LSD1:INSM1 interactions and de-repressing YAP1 silencing. Our data support the clinical development of LSD1 inhibitors for treating CRPC - especially the aggressive NE phenotype.
Statement of Significance: Neuroendocrine prostate cancer presents a clinical challenge due to the lack of effective treatments. Our research demonstrates that bomedemstat, a potent and selective LSD1 inhibitor, effectively combats neuroendocrine prostate cancer by downregulating the ASCL1- dependent NE transcriptional program and re-expressing YAP1.

DOI: https://doi.org/10.1101/2024.01.17.576106
Arch Pharm (Weinheim). 2024 Feb 08. e2300636

A virtual library of small molecules mimicking dipeptides.

Victor Jun Yu Lim, Hans-Dieter Gerber, Hannes Schihada, Van Tuan Trinh, Daniel Hilger, Olalla Vázquez, Peter Kolb.

  Virtual combinatorial libraries are prevalent in drug discovery due to improvements in the prediction of synthetic reactions that can be performed. This has gone hand in hand with the development of virtual screening capabilities to effectively screen the large chemical spaces spanned by exhaustive enumeration of reaction products. In this study, we generated a small-molecule dipeptide mimic library to target proteins binding small peptides. The library was created based on the general idea of peptide synthesis, that is, amino acid mimics were reacted in silico to form the dipeptide mimics, yielding 2,036,819 unique compounds. After docking calculations, two compounds from the library were synthesized and tested against WD repeat-containing protein 5 (WDR5) and histamine receptors H1 -H4 to evaluate whether these molecules are viable in assays. The compounds showed the highest potency at the histamine H3 receptor, with Ki values in the two-digit micromolar range.

Keywords:  dipeptide; docking; histamine receptors; peptidomimetic; virtual combinatorial library

DOI:  https://doi.org/10.1002/ardp.202300636
Acta Pharm Sin B. 2024 Feb;14(2): 881-892

Disulfide bridge-targeted metabolome mining unravels an antiparkinsonian peptide.

Zhiwu Tong, Xiahong Xie, Huiming Ge, Ruihua Jiao, Tingting Wang, Xincun Wang, Wenying Zhuang, Gang Hu, Renxiang Tan.

  Peptides are a particular molecule class with inherent attributes of some small-molecule drugs and macromolecular biologics, thereby inspiring continuous searches for peptides with therapeutic and/or agrochemical potentials. However, the success rate is decreasing, presumably because many interesting but less-abundant peptides are so scarce or labile that they are likely 'overlooked' during the characterization effort. Here, we present the biochemical characterization and druggability improvement of an unprecedented minor fungal RiPP (ribosomally synthesized and post-translationally modified peptide), named acalitide, by taking the relevant advantages of metabolomics approach and disulfide-bridged substructure which is more frequently imprinted in the marketed peptide drug molecules. Acalitide is biosynthetically unique in the macrotricyclization via two disulfide bridges and a protease (AcaB)-catalyzed lactamization of AcaA, an unprecedented precursor peptide. Such a biosynthetic logic was successfully re-edited for its sample supply renewal to facilitate the identification of the in vitro and in vivo antiparkinsonian efficacy of acalitide which was further confirmed safe and rendered brain-targetable by the liposome encapsulation strategy. Taken together, the work updates the mining strategy and biosynthetic complexity of RiPPs to unravel an antiparkinsonian drug candidate valuable for combating Parkinson's disease that is globally prevailing in an alarming manner.

Keywords:  Acalitide; Antiparkinsonian; Biosynthesis; Fungal RiPPs; Macrocyclic peptide

DOI:  https://doi.org/10.1016/j.apsb.2023.09.006
Bioorg Med Chem Lett. 2024 Feb 03. pii: S0960-894X(24)00045-3. [Epub ahead of print]100 129643

Design, synthesis and biological evaluation of novel cyclic malonamide derivatives as selective RIPK1 inhibitors.

József Levente Petró, Gyula Bényei, Péter Bana, Nikolett Linke, Ferenc Horti, Judit Eszter Szabó, Krisztina Katalin Szalai, Gábor Hornyánszky, István Greiner, János Éles.

  Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) plays a key role in cell death and inflammation. RIPK1 is a well-established therapeutic target, due to the presence of a unique kinase-regulating allosteric pocket, which enables selective inhibition. Herein we used GSK2982772 as our starting point in our discovery campaign. Applying isosteric replacement, we successfully identified the malonamide scaffold, instead of the well-established serine template. Further structural optimization led to the design and synthesis of a series of analog inhibitors. The enantiomers of the most promising compound were tested on 97 different kinases. The active enantiomer proved to be kinase selective.

Keywords:  Inhibitor; Malonamide; Necroptosis; RIPK1; Selectivity; Synthesis

DOI:  https://doi.org/10.1016/j.bmcl.2024.129643
Bioinformatics. 2024 Feb 05. pii: btae069. [Epub ahead of print]

PMIpred: a physics-informed web server for quantitative Protein-Membrane interaction prediction.

Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada.

MOTIVATION: Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structures are lacking, and such tools could greatly benefit the discovery of membrane-interacting motifs, as well as their de novo design.
RESULTS: Here, we trained a transformer neural network model on molecular dynamics data for >50,000 peptides that is able to accurately predict the (relative) membrane-binding free energy for any given amino acid sequence. Using this information, our physics-informed model is able to classify a peptide's membrane-associative activity as either non-binding, curvature sensing, or membrane binding. Moreover, this method can be applied to detect membrane-interaction regions in a wide variety of proteins, with comparable predictive performance as state-of-the-art data-driven tools like DREAMM, PPM3, and MODA, but with a wider applicability regarding protein diversity, and the added feature to distinguish curvature sensing from general membrane binding.
AVAILABILITY: We made these tools available as a web server, coined Protein-Membrane Interaction predictor (PMIpred), which can be accessed at https://pmipred.fkt.physik.tu-dortmund.de.

DOI: https://doi.org/10.1093/bioinformatics/btae069
Cancers (Basel). 2024 Jan 29. pii: 574. [Epub ahead of print]16(3):

The Oncogenic Lipid Sphingosine-1-Phosphate Impedes the Phagocytosis of Tumor Cells by M1 Macrophages in Diffuse Large B Cell Lymphoma.

Tracey A Perry, Navta Masand, Katerina Vrzalikova, Matthew Pugh, Wenbin Wei, Robert Hollows, Katerina Bouchalova, Mahdi Nohtani, Eanna Fennell, Jan Bouchal, Pamela Kearns, Paul G Murray.

   BACKGROUND: A total of 30-40% of diffuse large B cell lymphoma (DLBCL) patients will either not respond to the standard therapy or their disease will recur. The first-line treatment for DLBCL is rituximab and combination chemotherapy. This treatment involves the chemotherapy-induced recruitment of tumor-associated macrophages that recognize and kill rituximab-opsonized DLBCL cells. However, we lack insights into the factors responsible for the recruitment and functionality of macrophages in DLBCL tumors.
METHODS: We have studied the effects of the immunomodulatory lipid sphingosine-1-phosphate (S1P) on macrophage activity in DLBCL, both in vitro and in animal models.
RESULTS: We show that tumor-derived S1P mediates the chemoattraction of both monocytes and macrophages in vitro and in animal models, an effect that is dependent upon the S1P receptor S1PR1. However, S1P inhibited M1 macrophage-mediated phagocytosis of DLBCL tumor cells opsonized with the CD20 monoclonal antibodies rituximab and ofatumumab, an effect that could be reversed by an S1PR1 inhibitor.
CONCLUSIONS: Our data show that S1P signaling can modulate macrophage recruitment and tumor cell killing by anti-CD20 monoclonal antibodies in DLBCL. The administration of S1PR1 inhibitors could enhance the phagocytosis of tumor cells and improve outcomes for patients.

Keywords:  CD20 monoclonal antibodies; DLBCL; S1P; S1PR1; SPHK1; macrophages; ofatumumab; phagocytosis; rituximab

DOI:  https://doi.org/10.3390/cancers16030574
Cancers (Basel). 2024 Jan 30. pii: 594. [Epub ahead of print]16(3):

The Effect of Non-Overlapping Somatic Mutations in BRAF, NRAS, NF1, or CKIT on the Incidence and Outcome of Brain Metastases during Immune Checkpoint Inhibitor Therapy of Metastatic Melanoma.

Wolfram Samlowski.

  Previous studies suggested that somatic BRAF and NRAS mutations in metastatic melanoma increase the risk for brain metastases. The risk related to other non-overlapping "driver" mutations is unknown. We performed a retrospective evaluation of the incidence, timing, and outcome of brain metastases in a population of melanoma patients that underwent uniform next-gen sequencing. All patients were treated with initial checkpoint inhibitor therapy. Seventeen of 88 patients (20.0%) developed brain metastases. Eleven patients had brain metastases at diagnosis (12.9%). These were all patients with BRAF V600 or NF1 mutations. Only six patients with NRAS, NF1, KIT, or BRAF mutations (including fusions/internal rearrangements experienced delayed CNS progression following immunotherapy (7.1%)). No "quadruple negative" patient developed brain metastases. Patients with brain metastases at diagnosis had a better outcome than those with delayed intracranial progression. Current predictive markers, (LDH, tumor mutation burden, and PDL1) were poorly correlated with the development of brain metastases. Treatment with immunotherapy appears to reduce the incidence of brain metastases. Next-gen molecular sequencing of tumors in metastatic melanoma patients was useful in identifying genetic subpopulations with an increased or reduced risk of brain metastases. This may allow eventual personalization of screening strategies.

Keywords:  central nervous system; ipilimumab; nivolumab; pembrolizumab; “driver” mutation

DOI:  https://doi.org/10.3390/cancers16030594
iScience. 2024 Feb 16. 27(2): 108876

Exploring the substrate stereoselectivity and catalytic mechanism of nonribosomal peptide macrocyclization in surugamides biosynthesis.

Zeqian Du, Yinhao Ma, Yaoyao Shen, Xuefeng Jiang, Yongjun Zhou, Ting Shi.

  SurE, the first reported penicillin-binding protein-like thioesterase (PBP-like TE), is known as a new off-loading cyclase, which catalyzes heterochiral coupling in nonribosomal peptides (NRPs). However, the structural rationale for substrate stereoselectivity and enzymatic mechanism remains mysterious. Here, computational models, integrating MD simulations and QM/MM methods, unveiled SurE's substrate recognition and catalytic process. An oxyanion hole stabilized the C-terminal D-residue during recognition. Residue R446 anchored the substrate for macrocyclization. A vital hydrogen-bonding network (Y154, K66, N156), verified by mutation results, was responsible for the recognition of N-terminal L-residue and involvement in catalytic process with a calculated 19.4 kcal/mol energy barrier. Four novel-designed peptide precursors were effectively cyclized into cyclopeptides by SurE based on computational analysis. Our results provide a comprehensive understanding of SurE's catalytic mechanism and guiding design of versatile PBP-like TEs for novel macrocyclic NRPs.

Keywords:  Applied sciences; Biocatalysis; Biotechnology; Catalysis

DOI:  https://doi.org/10.1016/j.isci.2024.108876
Angew Chem Int Ed Engl. 2024 Feb 07. e202318632

NIR-II Conjugated Electrolytes as Biomimetics of Lipid Bilayers for In Vivo Liposome Tracking.

Yingying Meng, Ji Gao, Peirong Zhou, Xudong Qin, Miao Tian, Xiaohui Wang, Cheng Zhou, Kai Li, Fei Huang, Yong Cao.

  Liposomes serve as promising and versatile vehicles for drug delivery. Tracking these nanosized vesicles, particularly in vivo, is crucial for understanding their pharmacokinetics. This study introduces the design and synthesis of three new conjugated electrolyte (CE) molecules, which emit in the second near-infrared window (NIR-II), facilitating deeper tissue penetration. Additionally, these CEs, acting as biomimetics of lipid bilayers, demonstrate superior compatibility with lipid membranes compared to commonly used carbocyanine dyes like DiR. To counteract the aggregation-caused quenching effect, CEs employ a twisted backbone, as such their fluorescence intensities can effectively enhance after a fluorophore multimerization strategy. Notably, a "passive" method was employed to integrate CEs into liposomes during the liposome formation, and membrane incorporation efficiency was significantly promoted to nearly 100%. To validate the in vivo tracking capability, the CE-containing liposomes were functionalized with cyclic arginine-glycine-aspartic acid (cRGD) peptides, serving as tumor-targeting ligands. Clear fluorescent images visualizing tumor site in living mice were captured by collecting the NIR-II emission. Uniquely, these CEs exhibit additional emission peak in visible region, enabling in vitro subcellular analysis using routine confocal microscopy. These results underscore the potential of CEs as a new-generation of membrane-targeting probes to facilitate the liposome-based medicine research.

Keywords:  Conjugated Electrolyte; Dual-emission; Lipid Bilayers; Liposome Labeling; NIR-II

DOI:  https://doi.org/10.1002/anie.202318632
Comput Biol Chem. 2024 Jan 22. pii: S1476-9271(24)00009-4. [Epub ahead of print]109 108021

Deep2Pep: A deep learning method in multi-label classification of bioactive peptide.

Lihua Chen, Zhenkang Hu, Yuzhi Rong, Bao Lou.

  Functional peptides are easy to absorb and have low side effects, which has attracted increasing interest from pharmaceutical scientists. However, due to the limitations in the laboratory funding and human resources, it is difficult to screen the functional peptides from a large number of peptides with unknown functions. With the development of machine learning and Deep learning, the combination of computational methods and biological information provides an effective method for identifying peptide functions. To explore the value of multi-functional active peptides, a new deep learning method named Deep2Pep (Deep learning to Peptides) was constructed, which was based on sequence encoding, embedding, and language tokenizer. It can achieve predictions of peptides on antimicrobial, antihypertensive, antioxidant and antihyperglycemic by converting sequence information into digital vectors, combined BiLSTM, attention-residual algorithm, and BERT Encoder. The results showed that Deep2Pep had a Hamming Loss of 0.095, subset Accuracy of 0.737, and Macro F1-Score of 0.734. which outperformed other models. BiLSTM played a primary role in Deep2Pep, which BERT encoder was in an auxiliary position. Deep learning algorithms was used in this study to accurately predict the four active functions of peptides, and it was expected to provide effective references for predicting multi-functional peptides.

Keywords:  Attention; Bidirectional Encoder Representation from Transformers (BERT); Bioactive Peptide; Long short term memory (LSTM); Multi-label

DOI:  https://doi.org/10.1016/j.compbiolchem.2024.108021
Front Immunol. 2024 ;15 1310443

Bioactive peptides: an alternative therapeutic approach for cancer management.

Nooshin Ghadiri, Moslem Javidan, Shima Sheikhi, Özge Taştan, Alessandro Parodi, Ziwei Liao, Mehdi Tayybi Azar, Mazdak Ganjalıkhani-Hakemi.

  Cancer is still considered a lethal disease worldwide and the patients' quality of life is affected by major side effects of the treatments including post-surgery complications, chemo-, and radiation therapy. Recently, new therapeutic approaches were considered globally for increasing conventional cancer therapy efficacy and decreasing the adverse effects. Bioactive peptides obtained from plant and animal sources have drawn increased attention because of their potential as complementary therapy. This review presents a contemporary examination of bioactive peptides derived from natural origins with demonstrated anticancer, ant invasion, and immunomodulation properties. For example, peptides derived from common beans, chickpeas, wheat germ, and mung beans exhibited antiproliferative and toxic effects on cancer cells, favoring cell cycle arrest and apoptosis. On the other hand, peptides from marine sources showed the potential for inhibiting tumor growth and metastasis. In this review we will discuss these data highlighting the potential befits of these approaches and the need of further investigations to fully characterize their potential in clinics.

Keywords:  anticancer; bioactive peptide; cancer immunotherapy; cancer therapy; immunomodulation

DOI:  https://doi.org/10.3389/fimmu.2024.1310443