bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2024–01–14
twenty-two papers selected by
Henry Lamb, Queensland University of Technology
  1. An Autocatalytic Peptide Cyclase Improves Fidelity and Yield of Circular Peptides In Vivo and In Vitro.
  2. Selective inhibitors targeting Fis1/Mid51 protein-protein interactions protect against hypoxia-induced damage in cardiomyocytes.
  3. Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction.
  4. In-Bridge Stereochemistry: A Determinant of Stapled Peptide Conformation and Activity.
  5. GLP-1 derivatives with functional sequences transit and migrate through trigeminal neurons.
  6. Conformationally constrained cyclic grafted peptidomimetics targeting protein-protein interactions.
  7. Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists.
  8. Discovering peptide inhibitors of thrombin as a strategy for anticoagulation.
  9. Dissecting the geometric and hydrophobic constraints of stapled peptides.
  10. High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering.
  11. Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids.
  12. A new class of macrocyclic peptides.
  13. Rational design of peptide inhibitors targeting HSP90-CDC37 protein-protein interaction.
  14. Discovery of novel brain permeable human ACSS2 inhibitors for blocking breast cancer brain metastatic growth.
  15. De novo design of drug-binding proteins with predictable binding energy and specificity.
  16. Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System.
  17. Facilitated Transport of EGFR Inhibitors Plays an Important Role in Their Cellular Uptake.
  18. Applications of Bioactive Peptides in Dermatology.
  19. Targeting glial lipid metabolism to tackle neurodegeneration.
  20. The predictive and prognostic role of single nucleotide gene variants of PD-1 and PD-L1 in patients with advanced melanoma treated with PD-1 inhibitors.
  21. Unraveling the Puzzle of Therapeutic Peptides: A Promising Frontier in Huntington's Disease Treatment.
  22. Continuous Fluorescence Assay for In Vitro Translation Compatible with Noncanonical Amino Acids.
  1. ACS Synth Biol. 2024 Jan 09.
    An Autocatalytic Peptide Cyclase Improves Fidelity and Yield of Circular Peptides In Vivo and In Vitro.
    Noel Lacerna, Ying Cong, Eric W Schmidt.
      Peptide cyclization improves conformational rigidity, providing favorable pharmacological properties, such as proteolytic resistance, target specificity, and membrane permeability. Thus, many synthetic and biosynthetic peptide circularization strategies have been developed. PatG and related natural macrocyclases process diverse peptide sequences, generating millions of cyclic derivatives. However, the application of these cyclases is limited by low yields and the potential presence of unwanted intermediates. Here, we designed a covalently fused G macrocyclase with substrates that efficiently and spontaneously release cyclic peptides. To increase the fidelity of synthesis, we developed an orthogonal control mechanism enabling precision synthesis in Escherichia coli. As a result, a library comprising 4.8 million cyclic derivatives was constructed, producing an estimated 2.6 million distinct cyclic peptides with an improved yield and fidelity.
    Keywords:  autocatalysis; cyanobactins; cyclic peptide library
    DOI:  https://doi.org/10.1021/acssynbio.3c00645
  2. Front Pharmacol. 2023 ;14 1275370
    Selective inhibitors targeting Fis1/Mid51 protein-protein interactions protect against hypoxia-induced damage in cardiomyocytes.
    Mulate Zerihun, Nir Qvit.
      Cardiovascular diseases (CVDs) are the most common non-communicable diseases globally. An estimated 17.9 million people died from CVDs in 2019, representing 32% of all global deaths. Mitochondria play critical roles in cellular metabolic homeostasis, cell survival, and cell death, as well as producing most of the cell's energy. Protein-protein interactions (PPIs) have a significant role in physiological and pathological processes, and aberrant PPIs are associated with various diseases, therefore they are potential drug targets for a broad range of therapeutic areas. Due to their ability to mimic natural interaction motifs and cover relatively larger interaction region, peptides are very promising as PPI inhibitors. To expedite drug discovery, computational approaches are widely used for screening potential lead compounds. Here, we developed peptides that inhibit mitochondrial fission 1 (Fis1)/mitochondrial dynamics 51 kDa (Mid51) PPI to reduce the cellular damage that can lead to various human pathologies, such as CVDs. Based on a rational design approach we developed peptide inhibitors of the Fis1/Mid51 PPI. In silico and in vitro studies were done to evaluate the biological activity and molecular interactions of the peptides. Two peptides, CVP-241 and CVP-242 were identified based on low binding energy and molecular dynamics simulations. These peptides inhibit Fis1/Mid51 PPI (-1324.9 kcal mol-1) in docking calculations (CVP-241, -741.3 kcal mol-1, and CVP-242, -747.4 kcal mol-1), as well as in vitro experimental studies Fis1/Mid51 PPI (KD 0.054 µM) Fis1/Mid51 PPI + CVP-241 (KD 3.43 µM), and Fis1/Mid51 PPI + CVP-242 (KD 44.58 µM). Finally, these peptides have no toxicity to H9c2 cells, and they increase cell viability in cardiomyocytes (H9c2 cells). Consequently, the identified inhibitor peptides could serve as potent molecules in basic research and as leads for therapeutic development.
    Keywords:  cardiovascular diseases (CVDs); inhibitor; mitochondrial dynamics 51 kDa (Mid51); mitochondrial fission 1 (Fis1); peptide; protein-protein interaction (PPI)
    DOI:  https://doi.org/10.3389/fphar.2023.1275370
  3. Bioorg Med Chem Lett. 2024 Jan 05. pii: S0960-894X(24)00001-5. [Epub ahead of print] 129599
    Design of cyclic peptides as novel inhibitors of ICOS/ICOSL interaction.
    Somaya A Abdel-Rahman, Brianda L Santini, Laura Calvo-Barreiro, Martin Zacharias, Moustafa Gabr.
      Compared to small molecules and antibodies, cyclic peptides exhibit unique biochemical and therapeutic attributes in the realm of pharmaceutical applications. The interaction between the inducible costimulator (ICOS) and its ligand (ICOSL) plays a key role in T-cell differentiation and activation. ICOS/ICOSL inhibition results in a reduction in the promotion of immunosuppressive regulatory T cells (Tregs) in both hematologic malignancies and solid tumors. Herein, we implement the computational cPEPmatch approach to design the first examples of cyclic peptides that inhibit ICOS/ICOSL interaction. The top cyclic peptide from our approach possessed an IC50 value of 1.87 ± 0.15 μM as an ICOS/ICOSL inhibitor and exhibited excellent in vitro pharmacokinetic properties as a drug candidate. Our work will lay the groundwork for future endeavors in cancer drug discovery, with the goal of developing cyclic peptides that target the ICOS/ICOSL interaction.
    Keywords:  Computational chemistry; Cyclic peptides; ICOS; Immune checkpoints; Immunomodulators
    DOI:  https://doi.org/10.1016/j.bmcl.2024.129599
  4. Chembiochem. 2024 Jan 08. e202300747
    In-Bridge Stereochemistry: A Determinant of Stapled Peptide Conformation and Activity.
    Jingyi Zhang, Suwei Dong.
      Peptide side chain stapling has been proven to be an effective strategy for fine-tuning peptide properties. This innovative approach leads to the creation of stapled peptides characterized by stabilized α-helical conformations, enhanced protein-binding affinity, improved cell permeability, superior enzymatic stability, and numerous other advantages. Extensive research has explored the impact of various stapling bridges on the properties of these peptides, with limited investigation into the influence of bridge chirality, until very recently. In this concise review, we provide a brief overview of the current state of knowledge regarding the stereochemistry within the bridges of stapled peptides, offering insights into the potential applications of chiral bridges in the design and development of stapled peptides.
    Keywords:  helicity; in-bridge chirality; peptide properties; peptide stapling; target binding affinity
    DOI:  https://doi.org/10.1002/cbic.202300747
  5. Eur J Pharm Biopharm. 2024 Jan 05. pii: S0939-6411(24)00002-X. [Epub ahead of print] 114176
    GLP-1 derivatives with functional sequences transit and migrate through trigeminal neurons.
    Tomomi Akita, Mizuki Shimamura, Ayano Tezuka, Marina Takagi, Chikamasa Yamashita.
      Patients with dementia are increasing with the aging of the population, and dementia has become a disease with high unmet medical needs. Glucagon-like peptide-1 (GLP-1), a neuropeptide, has been reported to improve learning and memory following intracerebroventricular administration. We focused on intranasal administration, which can deliver drugs noninvasively and efficiently to the brain. Although much of the human nasal mucosa is occupied by respiratory epithelium, many capillaries are present in the paracellular route of respiratory epithelium. Therefore, to incorporate GLP-1 into cells, we created a GLP-1 derivative by adding cell-penetrating peptides (CPP) and penetration accelerating sequences (PAS) to GLP-1. We investigated in vitro and in vivo function of PAS-CPP-GLP-1 to enable the translocation of GLP-1 directly from nose to brain. PAS-CPP-GLP-1 enhanced cellular uptake by macropinocytosis with CPP, efficiently escaped from the endosomes due to PAS, and exited the cells. PAS-CPP-GLP-1 also transited trigeminal nerve cells through axon transport and migrated to the adjacent trigeminal nerve cell. Moreover, PAS-CPP-GLP-1 showed significant improvement in learning memory in mice within 20 min of intranasal administration. These results suggested CPP and PAS may be important for the efficient transfer of GLP-1 to the site of action in the brain following intranasal administration.
    Keywords:  Glucagon-like peptide-1; cell-penetrating peptide; intracellular dynamics; learning and memory; nose-to-brain system; penetration accelerating sequence
    DOI:  https://doi.org/10.1016/j.ejpb.2024.114176
  6. Pept Sci (Hoboken). 2023 Sep;pii: e24328. [Epub ahead of print]115(5):
    Conformationally constrained cyclic grafted peptidomimetics targeting protein-protein interactions.
    Achyut Dahal, Vivekanandan Subramanian, Prajesh Shrestha, Dong Liu, Ted Gauthier, Seetharama Jois.
      Sunflower trypsin inhibitor-1 (SFTI-1) structure is used for designing grafted peptides as a possible therapeutic agent. The grafted peptide exhibits multiple conformations in solution due to the presence of proline in the structure of the peptide. To lock the grafted peptide into a major conformation in solution, a dibenzofuran moiety (DBF) was incorporated in the peptide backbone structure, replacing the Pro-Pro sequence. NMR studies indicated a major conformation of the grafted peptide in solution. Detailed structural studies suggested that SFTI-DBF adopts a twisted beta-strand structure in solution. The surface plasmon resonance analysis showed that SFTI-DBF binds to CD58 protein. A model for the protein-SFTI-DBF complex was proposed based on docking studies. These studies suggested that SFTI-1 grafted peptide can be used to design stable peptides for therapeutic purposes by grafting organic functional groups and amino acids. However, when a similar strategy was used with another grafted peptide, the resulting peptide did not produce a single major conformation, and its biological activity was lost. Thus, conformational constraints depend on the sequence of amino acids used for SFTI-1 grafting.
    Keywords:  CD2; CD58; EGFR; Protein-protein interaction; grafted peptidomimetic; sunflower trypsin inhibitor
    DOI:  https://doi.org/10.1002/pep2.24328
  7. Nat Commun. 2024 Jan 12. 15(1): 489
    Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists.
    Arun Chandramohan, Hubert Josien, Tsz Ying Yuen, Ruchia Duggal, Diana Spiegelberg, Lin Yan, Yu-Chi Angela Juang, Lan Ge, Pietro G Aronica, Hung Yi Kristal Kaan, Yee Hwee Lim, Andrea Peier, Brad Sherborne, Jerome Hochman, Songnian Lin, Kaustav Biswas, Marika Nestor, Chandra S Verma, David P Lane, Tomi K Sawyer, Robert Garbaccio, Brian Henry, Srinivasaraghavan Kannan, Christopher J Brown, Charles W Johannes, Anthony W Partridge.
      Although stapled α-helical peptides can address challenging targets, their advancement is impeded by poor understandings for making them cell permeable while avoiding off-target toxicities. By synthesizing >350 molecules, we present workflows for identifying stapled peptides against Mdm2(X) with in vivo activity and no off-target effects. Key insights include a clear correlation between lipophilicity and permeability, removal of positive charge to avoid off-target toxicities, judicious anionic residue placement to enhance solubility/behavior, optimization of C-terminal length/helicity to enhance potency, and optimization of staple type/number to avoid polypharmacology. Workflow application gives peptides with >292x improved cell proliferation potencies and no off-target cell proliferation effects ( > 3800x on-target index). Application of these 'design rules' to a distinct Mdm2(X) peptide series improves ( > 150x) cellular potencies and removes off-target toxicities. The outlined workflow should facilitate therapeutic impacts, especially for those targets such as Mdm2(X) that have hydrophobic interfaces and are targetable with a helical motif.
    DOI:  https://doi.org/10.1038/s41467-023-43346-4
  8. Medicine (Baltimore). 2024 Jan 12. 103(2): e36849
    Discovering peptide inhibitors of thrombin as a strategy for anticoagulation.
    Shuxin Zhen, Guiping Wang, Xiaoli Li, Jing Yang, Jiaxin Yu, Yucong Wang.
      Unusual blood clots can cause serious health problems, such as lung embolism, stroke, and heart attack. Inhibiting thrombin activity was adopted as an effective strategy for preventing blood clots. In this study, we explored computational-based method for designing peptide inhibitors of human thrombin therapeutic peptides to prevent platelet aggregation. The random peptides and their 3-dimentional structures were generated to build a virtual peptide library. The generated peptides were docked into the binding pocket of human thrombin. The designed strong binding peptides were aligned with the native binder by comparative study, and we showed the top 5 peptide binders display strong binding affinity against human thrombin. The 5 peptides were synthesized and validated their inhibitory activity. Our result showed the 5-mer peptide AEGYA, EVVNQ, and FASRW with inhibitory activity against thrombin, range from 0.53 to 4.35 μM. In vitro anti-platelet aggregation assay was carried out, suggesting the 3 peptides can inhibit the platelet aggregation induced by thrombin. This study showed computer-aided peptide inhibitor design can be a robust method for finding potential binders for thrombin, which provided solutions for anticoagulation.
    DOI:  https://doi.org/10.1097/MD.0000000000036849
  9. Proteins. 2024 Jan 09.
    Dissecting the geometric and hydrophobic constraints of stapled peptides.
    Jianguo Li, Yaw Sing Tan, Chandra S Verma.
      Stapled peptides are a promising class of molecules with potential as highly specific probes of protein-protein interactions and as therapeutics. Hydrocarbon stapling affects the peptide properties through the interplay of two factors: enhancing the overall hydrophobicity and constraining the conformational flexibility. By constructing a series of virtual peptides, we study the role of each factor in modulating the structural properties of a hydrocarbon-stapled peptide PM2, which has been shown to enter cells, engage its target Mouse Double Minute 2 (MDM2), and activate p53. Hamiltonian replica exchange molecular dynamics (HREMD) simulations suggest that hydrocarbon stapling favors helical populations of PM2 through a combination of the geometric constraints and the enhanced hydrophobicity of the peptide. To further understand the conformational landscape of the stapled peptides along the binding pathway, we performed HREMD simulations by restraining the peptide at different distances from MDM2. When the peptide approaches MDM2, the binding pocket undergoes dehydration which appears to be greater in the presence of the stapled peptide compared with the linear peptide. In the binding pocket, the helicity of the stapled peptide is increased due to the favorable interactions between the peptide residues as well as the staple and the microenvironment of the binding pocket, contributing to enhanced affinity. The dissection of the multifaceted mechanism of hydrocarbon stapling into individual factors not only deepens fundamental understanding of peptide stapling, but also provides guidelines for the design of new stapled peptides.
    Keywords:  MDM2; molecular modeling and simulations; peptide-protein complex; secondary structure; stapled peptides
    DOI:  https://doi.org/10.1002/prot.26662
  10. ACS Synth Biol. 2024 Jan 09.
    High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering.
    Hannah N Fernandez, Ashley M Kretsch, Sylvia Kunakom, Adjo E Kadjo, Douglas A Mitchell, Alessandra S Eustáquio.
      The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in the plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated the plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery, we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery.
    Keywords:  Burkholderiaceae; RiPP; bacteria; heterologous expression; lasso peptide; natural product; secondary metabolite
    DOI:  https://doi.org/10.1021/acssynbio.3c00597
  11. Biochim Biophys Acta Biomembr. 2024 Jan 06. pii: S0005-2736(23)00150-5. [Epub ahead of print] 184268
    Molecular dynamics simulations support a preference of cyclotide kalata B1 for phosphatidylethanolamine phospholipids.
    Ras Baizureen Roseli, Yen-Hua Huang, Sónia Troeira Henriques, Quentin Kaas, David J Craik.
      Kalata B1 (kB1), a naturally occurring cyclotide has been shown experimentally to bind lipid membranes that contain phosphatidylethanolamine (PE) phospholipids. Here, molecular dynamics simulations were used to explore its interaction with two phospholipids, palmitoyloleoylphosphatidylethanolamine (POPE), palmitoyloleoylphosphatidylcholine (POPC), and a heterogeneous membrane comprising POPC/POPE (90:10), to understand the basis for the selectivity of kB1 towards PE phospholipids. The simulations showed that in the presence of only 10 % POPE lipid, kB1 forms a stable binding complex with membrane bilayers. An ionic interaction between the E7 carboxylate group of kB1 and the ammonium group of PE headgroups consistently initiates binding of kB1 to the membrane. Additionally, stable noncovalent interactions such as hydrogen bonding (E7, T8, V10, G11, T13 and N15), cation-π (W23), and CH-π (W23) interactions between specific residues of kB1 and the lipid membrane play an important role in stabilizing the binding. These findings are consistent with a structure-activity relationship study on kB1 where lysine mutagenesis on the bioactive and hydrophobic faces of the peptide abolished membrane-dependent bioactivities. In summary, our simulations suggest the importance of residue E7 (in the bioactive face) in enabling kB1 to recognize and bind selectively to PE-containing phospholipids bilayers through ionic and hydrogen bonding interactions, and of W23 (in the hydrophobic face) for the association and insertion of kB1 into the lipid bilayer through cation-π and CH-π interactions. Overall, this work enhances our understanding of the molecular basis of the membrane binding and bioactivity of this prototypic cyclotide.
    Keywords:  Cyclotide; Kalata B1; Molecular dynamics simulation; Phosphatidylcholine; Phosphatidylethanolamine; Selectivity
    DOI:  https://doi.org/10.1016/j.bbamem.2023.184268
  12. Nat Chem Biol. 2024 Jan 08.
    A new class of macrocyclic peptides.
    Krushnamurthy Pattanayakanahalli Henjarappa, Simita Das, Nilkamal Mahanta.
      
    DOI:  https://doi.org/10.1038/s41589-023-01507-y
  13. Future Med Chem. 2024 Jan 08.
    Rational design of peptide inhibitors targeting HSP90-CDC37 protein-protein interaction.
    Qiuyue Zhang, Ling Yan, Yuxuan Zhang, Lixiao Zhang, Jia Yu, Qidong You, Lei Wang.
      Background: Specifically blocking HSP90-CDC37 interaction is emerging as a prospective strategy for cancer therapy. Aim: Applying a kinase pseudopeptide rationale to the discovery of HSP90-CDC37 protein-protein interaction (PPI) inhibitors. Methods: Pseudosubstrates were identified through sequence alignment and evaluated by biolayer interferometry assay, co-immunoprecipitation assay and antiproliferation assay. Results: TAT-DDO-59120 was identified to disrupt HSP90-CDC37 PPI through directly binding to HSP90, both extracellularly and intracellularly. In addition, the identified peptide showed ideal antiproliferative activity against the colorectal cancer cell HCT116 (IC50 = 12.82 μM). Conclusion: Compared with the traditional method of screening a large compound library to identify PPI inhibitors, this method is rapid and efficient with strong purpose, which provides a novel strategy for designing HSP90-CDC37 PPI inhibitors.
    Keywords:  HSP90–CDC37 PPI inhibitor; pseudosubstrate; rational design; sequence alignment
    DOI:  https://doi.org/10.4155/fmc-2023-0320
  14. bioRxiv. 2023 Dec 23. pii: 2023.12.22.573073. [Epub ahead of print]
    Discovery of novel brain permeable human ACSS2 inhibitors for blocking breast cancer brain metastatic growth.
    Emily Esquea, Lorela Ciraku, Riley G Young, Jessica Merzy, Alexandra N Talarico, Adel Ahmed Rashad, Simon Cocklin, Nicole L Simone, Joris Beld, Mauricio J Reginato, Alexej Dick.
      Breast-cancer brain metastasis (BCBM) poses a significant clinical challenge, resulting in an end-stage diagnosis and hindered by limited therapeutic options. The blood-brain barrier (BBB) acts as an anatomical and physiological hurdle for therapeutic compounds, restricting the effective delivery of therapies to the brain. In order to grow and survive in a nutrient-poor environment, tumors in the brain must adapt to their metabolic needs, becoming highly dependent on acetate. These tumors rely on the conversion of acetate to acetyl-CoA by the enzyme Acetyl-CoA synthetase 2 (ACSS2), a key metabolic enzyme involved in regulating fatty acid synthesis and protein acetylation in tumor cells. ACSS2 has emerged as a crucial enzyme required for the growth of tumors in the brain. Here, we utilized a computational pipeline, combining pharmacophore-based shape screen methodology with ADME property predictions to identify novel brain-permeable ACSS2 inhibitors. From a small molecule library, this approach identified 30 potential ACSS2 binders, from which two candidates, AD-5584 and AD-8007, were validated for their binding affinity, predicted metabolic stability, and, notably, their ability to traverse the BBB. We show that treatment of BCBM cells, MDA-MB-231BR, with AD-5584 and AD-8007 leads to a significant reduction in lipid storage, reduction in colony formation, and increase in cell death in vitro . Utilizing an ex vivo orthotopic brain-slice tumor model, we show that treatment with AD-8007 and AD-5584 significantly reduces tumor size and synergizes with radiation in blocking BCBM tumor growth ex vivo. Importantly, we show that following intraperitoneal injections with AD-5584 and AD-8007, we can detect these compounds in the brain, confirming their BBB permeability. Thus, we have identified and validated novel ACSS2 inhibitor candidates for further drug development and optimization as agents for treating patients with breast cancer brain metastasis.
    DOI:  https://doi.org/10.1101/2023.12.22.573073
  15. bioRxiv. 2023 Dec 23. pii: 2023.12.23.573178. [Epub ahead of print]
    De novo design of drug-binding proteins with predictable binding energy and specificity.
    Lei Lu, Xuxu Gou, Sophia K Tan, Samuel I Mann, Hyunjun Yang, Xiaofang Zhong, Dimitrios Gazgalis, Jesús Valdiviezo, Hyunil Jo, Yibing Wu, Morgan E Diolaiti, Alan Ashworth, Nicholas F Polizzi, William F DeGrado.
      The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.
    One Sentence Summary: We use informatic sampling to design low nM drug-binding proteins, and physics-based calculations to accurately predict affinities.
    DOI:  https://doi.org/10.1101/2023.12.23.573178
  16. Int J Mol Sci. 2023 Dec 21. pii: 166. [Epub ahead of print]25(1):
    Comparative Analysis of Cyclization Techniques in Stapled Peptides: Structural Insights into Protein-Protein Interactions in a SARS-CoV-2 Spike RBD/hACE2 Model System.
    Sára Ferková, Ulrike Froehlich, Marie-Édith Nepveu-Traversy, Alexandre Murza, Taha Azad, Michel Grandbois, Philippe Sarret, Pierre Lavigne, Pierre-Luc Boudreault.
      Medicinal chemistry is constantly searching for new approaches to develop more effective and targeted therapeutic molecules. The design of peptidomimetics is a promising emerging strategy that is aimed at developing peptides that mimic or modulate the biological activity of proteins. Among these, stapled peptides stand out for their unique ability to stabilize highly frequent helical motifs, but they have failed to be systematically reported. Here, we exploit chemically diverse helix-inducing i, i + 4 constraints-lactam, hydrocarbon, triazole, double triazole and thioether-on two distinct short sequences derived from the N-terminal peptidase domain of hACE2 upon structural characterization and in silico alanine scan. Our overall objective was to provide a sequence-independent comparison of α-helix-inducing staples using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. We identified a 9-mer lactam stapled peptide derived from the hACE2 sequence (His34-Gln42) capable of reaching its maximal helicity of 55% with antiviral activity in bioreporter- and pseudovirus-based inhibition assays. To the best of our knowledge, this study is the first comprehensive investigation comparing several cyclization methods with the goal of generating stapled peptides and correlating their secondary structures with PPI inhibitions using a highly topical model system (i.e., the interaction of SARS-CoV-2 Spike RBD with hACE2).
    Keywords:  SARS-CoV-2; circular dichroism (CD); nuclear magnetic resonance (NMR); peptidomimetics; protein–protein interaction (PPI)
    DOI:  https://doi.org/10.3390/ijms25010166
  17. Anal Chem. 2024 Jan 12.
    Facilitated Transport of EGFR Inhibitors Plays an Important Role in Their Cellular Uptake.
    Brian S Wong, Erin L Dunnington, Ruibing Wu, Jonathan I Kim, Kailun Hu, Thomas H Ro, Dan Fu.
      Epidermal growth factor receptor (EGFR) is a transmembrane protein commonly targeted by tyrosine kinase inhibitors (TKIs) as a front-line therapy for patients with many cancers including nonsmall cell lung cancer (NSCLC). Effective treatment requires efficient intracellular drug uptake and target binding. However, despite the recent success in the development of new TKI drugs, the mechanisms of uptake for many TKIs are still poorly understood due to the difficulty in imaging and measuring nonfluorescent drug molecules at a subcellular resolution. It has previously been shown that weakly basic TKI drugs are sequestered in lysosomes. Leveraging this property, we apply hyperspectral stimulated Raman scattering imaging to directly visualize and quantify two Food and Drug Administration-approved EGFR inhibitor drugs (lapatinib and afatinib) inside living cells and the changes in their cellular uptake upon the addition of organic cation transporter inhibitors. These single-cell quantitative measurements provide new insight into the role of membrane transporters in the uptake of TKI drugs in living cells.
    DOI:  https://doi.org/10.1021/acs.analchem.3c04242
  18. J Drugs Dermatol. 2024 Jan 01. 23(1): 1369-1370
    Applications of Bioactive Peptides in Dermatology.
      
    DOI:  https://doi.org/10.36849/JDD.1223
  19. Nat Rev Drug Discov. 2024 Jan 10.
    Targeting glial lipid metabolism to tackle neurodegeneration.
    Katie Kingwell.
      
    DOI:  https://doi.org/10.1038/d41573-024-00004-8
  20. Immunooncol Technol. 2023 Dec;20 100408
    The predictive and prognostic role of single nucleotide gene variants of PD-1 and PD-L1 in patients with advanced melanoma treated with PD-1 inhibitors.
    A Boutros, R Carosio, D Campanella, F Spagnolo, B Banelli, A Morabito, M P Pistillo, E Croce, F Cecchi, P Pronzato, P Queirolo, E Raposio, V Fontana, E T Tanda.
       Background: Despite having revolutionized the treatment paradigm for advanced melanoma, not all patients benefit from immune checkpoint inhibitor therapy. To date, there are no predictive biomarkers for response or the occurrence of immune-related adverse events (irAEs) to programmed cell death protein 1 (PD-1) inhibitors. Our aim was to investigate the predictive and prognostic role of single nucleotide variants (SNVs) of genes involved in the PD-1 axis.
    Methods: We analysed, in metastatic melanoma patients treated with nivolumab or pembrolizumab, five PD-1 SNVs, namely PD1.3 G>A (rs11568821), PD1.5 C>T (rs2227981), PD1.6 G>A (rs10204525), PD1.7 T>C(rs7421861), PD1.10 C>G (rs5582977) and three programmed death-ligand 1 (PD-L1) SNVs: +8293 C>A (rs2890658), PD-L1 C>T (rs2297136) and PD-L1 G>C (rs4143815). Association of SNV genotypic frequencies with best overall response to PD-1 inhibitors and development of irAEs were estimated through a modified Poisson regression. A Cox regression modelling approach was applied to evaluate the SNV association with OS.
    Results: A total of 125 patients with advanced melanoma were included in the analysis. A reduction in irAEs risk was observed in patients carrying the PD-L1 +8293 C/A genotype compared with those carrying the C/C genotype (risk ratio = 0.45; 95% CL 0.22-0.93; P = 0.031). A trend for a reduction in irAEs was also observed with the PD1.5 T allele (risk ratio = 0.70, 95% confidence limits 0.48-1.01 versus C allele). None of the SNVs was associated with response to therapy. Finally, a survival benefit was observed in patients harbouring the PD1.7 C/C genotype (hazard ratio = 0.37; 95% confidence limits 0.14-0.96; P = 0.028) in the homozygous model.
    Conclusions: Our study showed that PD-1.5 and PD-L1 +8293 SNVs may play a role as a predictive biomarker of development of irAEs to PD-1 inhibitors. PD1.7 SNV may also be associated with a reduction of the risk of death, although further translational research is needed to confirm these results.
    Keywords:  PD-1; PD-L1; SNV; melanoma; single nucleotide gene variant
    DOI:  https://doi.org/10.1016/j.iotech.2023.100408
  21. J Med Chem. 2024 Jan 11.
    Unraveling the Puzzle of Therapeutic Peptides: A Promising Frontier in Huntington's Disease Treatment.
    Shakir Ahamad, Nargis Bano, Sameera Khan, Mohd Kamil Hussain, Shahnawaz A Bhat.
      Huntington's disease (HD) is a neurodegenerative genetic disorder characterized by a mutation in the huntingtin (HTT) gene, resulting in the production of a mutant huntingtin protein (mHTT). The accumulation of mHTT leads to the development of toxic aggregates in neurons, causing cell dysfunction and, eventually, cell death. Peptide therapeutics target various aspects of HD pathology, including mHTT reduction and aggregation inhibition, extended CAG mRNA degradation, and modulation of dysregulated signaling pathways, such as BDNF/TrkB signaling. In addition, these peptide therapeutics also target the detrimental interactions of mHTT with InsP3R1, CaM, or Caspase-6 proteins to mitigate HD. This Perspective provides a detailed perspective on anti-HD therapeutic peptides, highlighting their design, structural characteristics, neuroprotective effects, and specific mechanisms of action. Peptide therapeutics for HD exhibit promise in preclinical models, but further investigation is required to confirm their effectiveness as viable therapeutic strategies, recognizing that no approved peptide therapy for HD currently exists.
    DOI:  https://doi.org/10.1021/acs.jmedchem.3c01131
  22. ACS Synth Biol. 2024 Jan 09.
    Continuous Fluorescence Assay for In Vitro Translation Compatible with Noncanonical Amino Acids.
    Gianna N Kerestesy, Kara K Dods, Clinton A L McFeely, Matthew C T Hartman.
      The tolerance of the translation apparatus toward noncanonical amino acids (ncAAs) has enabled the creation of diverse natural-product-like peptide libraries using mRNA display for use in drug discovery. Typical experiments testing for ribosomal ncAA incorporation involve radioactive end point assays to measure yield alongside mass spectrometry experiments to validate incorporation. These end point assays require significant postexperimental manipulation for analysis and prevent higher throughput analysis and optimization experiments. Continuous assays for in vitro translation involve the synthesis of fluorescent proteins which require the full complement of canonical AAs for function and are therefore of limited utility for testing of ncAAs. Here, we describe a new, continuous fluorescence assay for in vitro translation based on detection of a short peptide tag using an affinity clamp protein, which exhibits changes in its fluorescent properties upon binding. Using this assay in a 384-well format, we were able to validate the incorporation of a variety of ncAAs and also quickly test for the codon reading specificities of a variety of Escherichia coli tRNAs. This assay enables rapid assessment of ncAAs and optimization of translation components and is therefore expected to advance the engineering of the translation apparatus for drug discovery and synthetic biology.
    Keywords:  affinity clamp; continuous assay; fluorescent proteins; in vitro translation; noncanonical amino acids; tRNA
    DOI:  https://doi.org/10.1021/acssynbio.3c00353
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