bims-cepepe Biomed News
on Cell-penetrating peptides
Issue of 2024–12–22
sixteen papers selected by
Henry Lamb, Queensland University of Technology
  1. Discovering covalent cyclic peptide inhibitors of peptidyl arginine deiminase 4 (PADI4) using mRNA-display with a genetically encoded electrophilic warhead.
  2. Designing Highly Potent Side-Chain Lactam-Bridged Cyclic Competence-Stimulating Peptide-Based Quorum-Sensing Modulators in Streptococcus oligofermentans.
  3. Non-symmetric cysteine stapling in native peptides and proteins.
  4. Evaluating the impact of cell-penetrating motif position on the cellular uptake of magnetite nanoparticles.
  5. A High-Throughput Method for Screening Peptide Activators of G-Protein-Coupled Receptors.
  6. Molecular Investigation of SNAC as an Oral Peptide Permeation Enhancer in Lipid Membranes via Solid-State NMR.
  7. Impact of Linker Composition on VHL PROTAC Cell Permeability.
  8. Disulfide-Directed Multicyclic Peptides with N-Terminally Extendable α-Helices for Recognition and Activation of G Protein-Coupled Receptors.
  9. Exploring Multivalency in the Development of Anti-PD-L1 Peptides for Cancer Immunotherapy.
  10. Late-Stage Reshaping of Phage-Displayed Libraries to Macrocyclic and Bicyclic Landscapes using a Multipurpose Linchpin.
  11. New Conjugates of Vancomycin with Cell-Penetrating Peptides-Synthesis, Antimicrobial Activity, Cytotoxicity, and BBB Permeability Studies.
  12. Design of pseudosymmetric protein hetero-oligomers.
  13. Tumor-Targeted Cell-Penetrating Peptides Reveal That Monomethyl Auristatin E Temporally Modulates the Tumor Immune Microenvironment.
  14. High-throughput discovery and deep characterization of cyclin-CDK docking motifs.
  15. Prediction of peptide structural conformations with AlphaFold2.
  16. Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties.
  1. Commun Chem. 2024 Dec 19. 7(1): 304
    Discovering covalent cyclic peptide inhibitors of peptidyl arginine deiminase 4 (PADI4) using mRNA-display with a genetically encoded electrophilic warhead.
    Isabel R Mathiesen, Ewen D D Calder, Simone Kunzelmann, Louise J Walport.
      Covalent drugs can achieve high potency with long dosing intervals. However, concerns remain about side-effects associated with off-target reactivity. Combining macrocyclic peptides with covalent warheads provides a solution to minimise off-target reactivity: the peptide enables highly specific target binding, positioning a weakly reactive warhead proximal to a suitable residue in the target. Here we demonstrate the direct discovery of covalent cyclic peptides using encoded libraries containing a weakly electrophilic cysteine-reactive fluoroamidine warhead. We combine direct incorporation of the warhead into peptide libraries using the flexible in vitro translation system with a peptide selection approach that identifies only covalent target binders. Using this approach, we identify potent and selective covalent inhibitors of the peptidyl arginine deiminase, PADI4 or PAD4, that react exclusively at the active site cysteine. We envisage this approach will enable covalent peptide inhibitor discovery for a range of related enzymes and expansion to alternative warheads in the future.
    DOI:  https://doi.org/10.1038/s42004-024-01388-9
  2. ACS Infect Dis. 2024 Dec 17.
    Designing Highly Potent Side-Chain Lactam-Bridged Cyclic Competence-Stimulating Peptide-Based Quorum-Sensing Modulators in Streptococcus oligofermentans.
    Uttam Ghosh, Yftah Tal-Gan.
      Streptococcus oligofermentans, a Gram-positive bacterium found in the oral microbiome, shows promise as an oral probiotic for preventing dental caries. It exhibits a reverse correlation with Streptococcus mutans, a key caries-causing pathogen, likely due to its production of hydrogen peroxide, a process mediated by quorum sensing (QS). In this work, we set out to develop novel lactam-based cyclic analogues of the competence stimulating peptide (CSP) signal utilized by S. oligofermentans for QS activation. To this end, we first conducted a ring position scan, where we determined the best positions within the CSP sequence to use for macrolactamization. We then conducted systematic ring size and bridge position scans to fine-tune the cyclic peptide conformation and identified a cyclic analogue, CSP-cyc(K2E2), with enhanced biological activity, 7-fold more active than the native CSP signal. This analogue also exhibited improved stability toward enzymatic degradation, demonstrating this analogue's potential utility as a chemical probe to study interspecies interactions between oral microbes and as a potential therapeutic agent. Overall, our lead cyclic analogue could be applied to augment the biotherapeutic potential of S. oligofermentans against S. mutans infections.
    Keywords:  Streptococcus oligofermentans; antivirulence; competence stimulating peptide; conformational screening; cyclic peptides; quorum sensing
    DOI:  https://doi.org/10.1021/acsinfecdis.4c00773
  3. Chem Commun (Camb). 2024 Dec 16.
    Non-symmetric cysteine stapling in native peptides and proteins.
    Sven Ullrich, Bishvanwesha Panda, Upamali Somathilake, Douglas J Lawes, Christoph Nitsche.
      Stapling rigidifies peptides through covalent linkages between amino acids. We introduce 2-chloromethyl-6-cyanopyridine for non-symmetric stapling of N-terminal and internal cysteines. This biocompatible method produces diverse peptide macrocycles with enhanced affinity, stability and inhibitory potency. It is applicable to native peptides and proteins alike, demonstrating potential for peptide drug discovery platforms.
    DOI:  https://doi.org/10.1039/d4cc04995k
  4. Front Bioeng Biotechnol. 2024 ;12 1450694
    Evaluating the impact of cell-penetrating motif position on the cellular uptake of magnetite nanoparticles.
    Laura Salgado, Paula C Cifuentes-Delgado, Juan Camilo Orozco, Carolina Muñoz-Camargo, Luis H Reyes, Valentina Quezada, Juan C Cruz.
      Cell-penetrating peptides (CPPs) have been employed to enhance the cellular uptake and intracellular delivery of various nanocarriers. Among them, nanoparticles (NPs) have been used as suitable vehicles for delivering different bioactive molecules in the treatment of a diverse range of diseases. Given the pivotal role of the conjugation method of CPPs, this study aims to evaluate the impact of the position of a cell-penetrating motif (LFVCR) on the biocompatibility, cellular uptake, and endosomal escape of magnetite NPs. The designed peptide's physicochemical properties suggest they are well-suited for efficient cell penetration with minimal cytotoxicity. The resulting designed nanoconjugates were characterized using Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), dynamic light scattering (DLS), and transmission electron microscopy (TEM). The results indicate that motif position significantly impacts the cellular uptake and endosomal escape of the designed nanobioconjugates. Key findings suggest that motif exposure enhances endocytosis-mediated cell internalization and improves endosomal escape efficiency. These results were compared with nanobioconjugates displaying previously reported CPPs. The selected nanobioconjugate demonstrated superior performance in endosomal escape and comparable cell uptake to the reference nanobioconjugates. These results, along with the nanobioconjugate's physicochemical characteristics and high biocompatibility, position the nanocarrier as a suitable candidate for delivering diverse bioactive molecules.
    Keywords:  cell-penetrating motif; cell-penetrating peptides; clathrin-mediated endocytosis; energy-dependent cellular uptake; magnetite nanoparticles
    DOI:  https://doi.org/10.3389/fbioe.2024.1450694
  5. ACS Omega. 2024 Dec 10. 9(49): 48471-48479
    A High-Throughput Method for Screening Peptide Activators of G-Protein-Coupled Receptors.
    Yagya Prasad Paudel, Pedro A Valiente, Jisun Kim, Philip M Kim.
      Here, we describe an innovative and efficient method for screening peptide activators of G-protein-coupled receptors (GPCRs) utilizing a protein-protein interaction (PPI) approach. We designed a library of 92,918 peptides fused with transmembrane domains of glycosylphosphatidylinositol-anchored proteins (GPI-APs). We employed a pooled lentiviral system to promote the expression of these proteins at the cellular membrane and evaluate their ability to activate GPCRs. We then used fluorescence-activated cell sorting (FACS) to screen the GPI-AP-peptide library and identify novel peptide activators of the glucagon-like peptide-1 receptor (GLP-1R). We discovered one peptide PepA3 derived from the Frizzled-like (FZ) domain of human Carboxypeptidase Z (CPZ), a regulated secreted metallocarboxypeptidase. Notably, PepA3 and its two related variants, PepA and PepA2, activated the GLP-1R receptor with less potency but comparable efficacy to that of GLP-1. We then hypothesized that all of these peptides will bind differently to the GLP-1R than the normal ligand. Our technology could identify novel GPCR-activating peptides for structure-function or drug discovery research.
    DOI:  https://doi.org/10.1021/acsomega.4c07071
  6. Mol Pharm. 2024 Dec 17.
    Molecular Investigation of SNAC as an Oral Peptide Permeation Enhancer in Lipid Membranes via Solid-State NMR.
    Jing Ling, Ryan Schroder, W Peter Wuelfing, John Higgins, Filippos Kesisoglou, Allen C Templeton, Yongchao Su.
      Oral peptide therapeutics are increasingly favored in the pharmaceutical industry for their ease of use and better patient adherence. However, they face challenges with poor oral bioavailability due to their high molecular weight and surface polarity. Permeation enhancers (PEs) like salcaprozate sodium (SNAC) have shown promise in clinical trials, achieving about 1% bioavailability. One proposed mechanism for enhancing permeation is membrane perturbation or fluidization, though direct experimental proof and quantitative analysis of these effects are still needed. This study employs solid-state NMR (ssNMR) to investigate how SNAC interacts with hydrated DMPC liposomes, measuring enhancements in membrane fluidity across interfacial and transmembrane regions. The methodology involves analyzing phosphate lipid headgroups and acyl chains using static 31P chemical shift anisotropy and 2H quadrupolar coupling measurements alongside 1H and 13C magic angle spinning NMR for motional averaging of 1H-1H and 1H-13C dipolar couplings. Our findings indicate an overall increase in the uniaxial motion of phospholipids with SNAC in a PE concentration-dependent manner. It boosts lipid headgroup dynamics and enhancement plateaus at 25% between 24 and 72 mM concentrations. SNAC effectively enhances the fluidity of the hydrophobic center by 43% at 72 mM PE concentration, more significantly than the interfacial region. It is worth noting that the extent of liposome dissolution and conversion to micelles increases as SNAC concentration rises. Including a model peptide drug, octreotide, introduces a competitive equilibrium in this complex PE-lipid-peptide system, further influencing membrane dynamics for peptide permeation. Interestingly, the membrane enhancement does not show the expected plateau, and a less significant lipid mobility increase is observed in the presence of octreotide, suggesting a less substantial impact compared to peptide-free systems, which is likely due to peptide-PE interactions that consume monomeric SNAC, reducing its interaction with the lipid membrane. This study provides the first quantitative and site-specific ssNMR measurements of membrane mobility influenced by one representative PE as a snapshot of PE lipid interaction in a liposome model, demonstrating how peptide drugs modulate competitive equilibria and PE-induced lipid dynamics.
    Keywords:  DMPC liposomes; SNAC; lipid dynamics; membrane fluidization; oral peptide delivery; permeation enhancer; solid-state NMR
    DOI:  https://doi.org/10.1021/acs.molpharmaceut.4c01061
  7. J Med Chem. 2024 Dec 18.
    Impact of Linker Composition on VHL PROTAC Cell Permeability.
    Yordanos Esubalew Abeje, Lianne H E Wieske, Vasanthanathan Poongavanam, Stefanie Maassen, Yoseph Atilaw, Philipp Cromm, Lutz Lehmann, Mate Erdelyi, Daniel Meibom, Jan Kihlberg.
      The discovery of cell permeable and orally bioavailable von Hippel-Lindau (VHL) proteolysis targeting chimeras (PROTACs) is challenging as their structures locates them at, or beyond, the outer limits of oral druggable space. We have designed a set of nine VHL PROTACs and found that the linker had a profound impact on passive cell permeability. Determination of the solution ensembles in a nonpolar solvent revealed that high permeability was correlated to the ability of the PROTACs to adopt folded conformations that have a low solvent accessible 3D polar surface area. Our results suggest that the design of cell permeable VHL PROTACs could focus on linkers that facilitate shielding of polar surface area in the VHL ligand in a nonpolar but not in a polar environment. In addition, we found that not only intramolecular hydrogen bonds, but also NH-π and π-π interactions contribute to the stabilization of low-polarity conformations, and thereby to high cell permeability.
    DOI:  https://doi.org/10.1021/acs.jmedchem.4c02492
  8. J Am Chem Soc. 2024 Dec 17.
    Disulfide-Directed Multicyclic Peptides with N-Terminally Extendable α-Helices for Recognition and Activation of G Protein-Coupled Receptors.
    Shihui Fan, Jie Li, Jie Zhuang, Qingtong Zhou, Yiting Mai, Bingni Lin, Ming-Wei Wang, Chuanliu Wu.
      Many peptide hormones adopt long α-helical structures upon interacting with their cognate receptors but often exhibit flexible conformations when unbound. Strategies that can stabilize long α-helices without disrupting their binding to receptors are still lacking, which hinders progress in their biological applications and drug development. Here, we present an approach that combines rational design with library screening to create and identify a unique disulfide-directed multicyclic peptide (DDMP) scaffold, which could effectively stabilize N-terminally extendable α-helices while displaying exceptional efficiency in disulfide pairing and oxidative folding. This DDMP scaffold was then utilized for stabilizing the α-helical structure of glucagon-like peptide-1 (GLP-1), resulting in a potent GLP-1 receptor (GLP-1R) agonist with a significantly improved α-helicity and proteolytic stability. By incorporating external α-helices into the DDMP scaffold, we can effectively preserve the native N-terminal α-helical structures while allowing for extensive evolution of the C-terminal disulfide-rich domain for enhancing target binding, as demonstrated by the generation of the DDMP-stabilized GLP-1 (g1:Ox). The cryo-electron microscopy structure of the g1:Ox-GLP-1R in complex with heterotrimeric Gs reveals the molecular basis for the potent binding between g1:Ox and GLP-1R. Specifically, the DDMP moiety establishes additional interactions with the extracellular domain of GLP-1R, which are absent in the case of GLP-1. Thus, this work offers a novel and effective approach for engineering therapeutic peptides and other peptide α-helices, ensuring that both the N- and C-terminal regions remain essential for target recognition and activation.
    DOI:  https://doi.org/10.1021/jacs.4c12808
  9. Pharm Res. 2024 Dec 17.
    Exploring Multivalency in the Development of Anti-PD-L1 Peptides for Cancer Immunotherapy.
    Umar-Farouk Mamani, Mohammed Nurudeen Ibrahim, Yanli Liu, John Fetse, Chien-Yu Lin, Sashi Kandel, Maryam Nakhjiri, Sushil Koirala, Yuhan Guo, Mohammed Alahmari, Kun Cheng.
       PURPOSE: The PD-1/PD-L1 pathway is one of the most effective immune checkpoint pathways utilized for cancer immunotherapy. Despite the success of anti-PD-1/PD-L1 mAbs, there is growing interest in developing low molecular weight anti-PD-1/PD-1 agents, such as peptides, because of their improved tumor penetration. We recently developed a small anti-PD-L1 peptide and demonstrated its promising anti-tumor activity. In this study, we investigate multivalency as a strategy to increase the binding avidity and blocking efficiency of the anti-PD-L1 peptide.
    METHODS: Multivalent peptide inhibitors are designed with multiple copies of a peptide inhibitor in a single molecule. We synthesized peptides with different valences and examined their activity. We also investigated how spacer length affects the activity of these multivalent peptides.
    RESULTS: Using this strategy, we developed a multivalent peptide that demonstrated approximately 40 times higher blocking efficiency and improved stability compared to the original peptide. Increasing the valency enhanced the peptide's specificity, which is essential for minimizing side effects.
    CONCLUSIONS: Multivalency approach represents a promising platform for improving the efficacy of peptide-based checkpoint inhibitors.
    Keywords:  anti-PD-L1; checkpoint inhibitor; immunotherapy; multivalency; peptide
    DOI:  https://doi.org/10.1007/s11095-024-03803-1
  10. J Am Chem Soc. 2024 Dec 19.
    Late-Stage Reshaping of Phage-Displayed Libraries to Macrocyclic and Bicyclic Landscapes using a Multipurpose Linchpin.
    Kejia Yan, Mark Miskolzie, Fernando Banales Mejia, Chuanhao Peng, Arunika I Ekanayake, Alexey Atrazhev, Jessica Cao, Dustin J Maly, Ratmir Derda.
      Genetically encoded libraries (GEL) are increasingly being used for the discovery of ligands for "undruggable" targets that cannot be addressed with small molecules. Foundational GEL platforms like phage-, yeast-, ribosome-, and mRNA-display have enabled the display of libraries composed of 20 natural amino acids (20AA). Unnatural amino acids (UAA) and chemical post-translational modification (cPTM) expanded GEL beyond the 20AA space to yield unnatural linear, cyclic, and bicyclic peptides. The standard operating procedure incorporates UAA and cPTM into a "naive" library with 108-1012 compounds and uses a chemically upgraded library in multiple rounds of selection to discover target-binding hits. However, such an approach uses zero knowledge of natural peptide-receptor interactions that might have been discovered in selections performed with 20AA libraries. There is currently no consensus regarding whether "zero-knowledge" naive libraries or libraries with pre-existing knowledge can offer a more effective path to discovery of molecular interactions. In this manuscript, we evaluated the feasibility of discovery of macrocyclic and bicyclic peptides from "nonzero-knowledge" libraries. We approach this problem by late-stage chemical reshaping of a preselected phage-displayed landscape of 20AA binders to NS3aH1 protease. The reshaping is performed using a novel multifunctional C2-symmetric linchpin, 3,5-bis(bromomethyl)benzaldehyde (termed KYL), that combines two electrophiles that react with thiols and an aldehyde group that reacts with N-terminal amine. KYL diversified phage-displayed peptides into bicyclic architectures and delineated 2 distinct sequence populations: (i) peptides with the HXDMT motif that retained binding upon bicyclization and (ii) peptides without the HXDMT motif that lost binding once chemically modified. The same HXDMT family can be found in traditional selections starting from the naive KYL-modified library. Our report provides a case study for discovering advanced, chemically upgraded macrocycles and bicycles from libraries with pre-existing knowledge. The results imply that other selection campaigns completed in 20AA space, potentially, can serve for late-stage reshaping and as a starting point for the discovery of advanced peptide-derived ligands.
    DOI:  https://doi.org/10.1021/jacs.4c13561
  11. Molecules. 2024 Nov 22. pii: 5519. [Epub ahead of print]29(23):
    New Conjugates of Vancomycin with Cell-Penetrating Peptides-Synthesis, Antimicrobial Activity, Cytotoxicity, and BBB Permeability Studies.
    Jarosław Ruczyński, Katarzyna Prochera, Natalia Kaźmierczak, Katarzyna Kosznik-Kwaśnicka, Lidia Piechowicz, Piotr Mucha, Piotr Rekowski.
      Vancomycin (Van) is a glycopeptide antibiotic commonly used as a last resort for treating life-threatening infections caused by multidrug-resistant bacterial strains, such as Staphylococcus aureus and Enterococcus spp. However, its effectiveness is currently limited due to the rapidly increasing number of drug-resistant clinical strains and its inherent cytotoxicity and poor penetration into cells and specific regions of the body, such as the brain. One of the most promising strategies to enhance its efficacy appears to be the covalent attachment of cell-penetrating peptides (CPPs) to the Van structure. In this study, a series of vancomycin conjugates with CPPs-such as TP10, Tat (47-57), PTD4, and Arg9-were designed and synthesized. These conjugates were tested for antimicrobial activity against four reference strains (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Pseudomonas aeruginosa) and two clinical drug-resistant strains: methicillin-resistant S. aureus and vancomycin-resistant E. faecium. In addition, cytotoxicity tests (using a human fibroblast cell line) and blood-brain barrier (BBB) permeability tests (using a parallel artificial membrane permeability assay-PAMPA-BBB assay) were conducted for selected compounds. Our research demonstrated that conjugation of Van with CPPs, particularly with Tat (47-57), Arg9, or TP10, significantly enhances its antimicrobial activity against Gram-positive bacteria such as S. aureus and Enterococcus spp., reduces its cytotoxicity, and improves its access to brain tissues. We conclude that these findings provide a strong foundation for the design of novel antimicrobial agents effective in treating infections caused by drug-resistant staphylococcal and enterococcal strains, while also being capable of crossing the BBB.
    Keywords:  PAMPA-BBB assay; Van-CPP conjugates; antimicrobial assay; antimicrobial peptides; cell-penetrating peptides; click chemistry; cytotoxicity assay; vancomycin
    DOI:  https://doi.org/10.3390/molecules29235519
  12. Nat Commun. 2024 Dec 18. 15(1): 10684
    Design of pseudosymmetric protein hetero-oligomers.
    Ryan D Kibler, Sangmin Lee, Madison A Kennedy, Basile I M Wicky, Stella M Lai, Marius M Kostelic, Ann Carr, Xinting Li, Cameron M Chow, Tina K Nguyen, Lauren Carter, Vicki H Wysocki, Barry L Stoddard, David Baker.
      Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials. However, the de novo design of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging unsolved problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign tasks, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting from de novo designed circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 19 new homo-oligomers and structurally recombined them to make 24 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system have identical or nearly identical backbones, and hence are ideal building blocks for generating and functionalizing larger symmetric and pseudosymmetric assemblies.
    DOI:  https://doi.org/10.1038/s41467-024-54913-8
  13. Molecules. 2024 Nov 27. pii: 5618. [Epub ahead of print]29(23):
    Tumor-Targeted Cell-Penetrating Peptides Reveal That Monomethyl Auristatin E Temporally Modulates the Tumor Immune Microenvironment.
    Mahsa Mortaja, Marcus M Cheng, Alina Ali, Jacqueline Lesperance, Dina V Hingorani, Mike M Allevato, Kanika Dhawan, Maria F Camargo, Rana R McKay, Stephen R Adams, J Silvio Gutkind, Sunil J Advani.
      Chemotherapies remain standard therapy for cancers but have limited efficacy and cause significant side effects, highlighting the need for targeted approaches. In the progression of cancer, tumors increase matrix metalloproteinase (MMP) activity. Leveraging and therapeutically redirecting tumor MMPs through activatable cell-penetrating peptide (ACPP) technology offers new approaches for tumor-selective drug delivery and for studying how drug payloads engage the tumor immune microenvironment. ACPPs are biosensing peptides consisting of a drug-conjugated polycationic cell-penetrating peptide masked by an autoinhibitory polyanionic peptide through an interlinking peptide linker. Since tumors overexpress MMPs, ACPP tumor-targeting is achieved using an MMP cleavable linker. Monomethyl auristatin E (MMAE) is a potent anti-tubulin and common drug payload in antibody drug conjugates; however there are limited pre-clinical studies on how this clinically effective drug modulates the interplay of cancer cells and the immune system. Here, we report the versatility of ACPP conjugates in syngeneic murine cancer models and interrogate how MMAE temporally alters the tumor immune microenvironment. We show that cRGD-ACPP-MMAE preferentially delivered MMAE to tumors in murine models. Targeted cRGD-ACPP-MMAE demonstrated anti-tumor kill activity that activated the innate and adaptive arms of the immune system. Understanding how targeted MMAE engages tumors can optimize MMAE tumor kill activity and inform rational combinations with other cancer therapeutics.
    Keywords:  anti-tubulins; cell-penetrating peptides; matrix metalloproteinases; peptide–drug conjugates
    DOI:  https://doi.org/10.3390/molecules29235618
  14. bioRxiv. 2024 Dec 04. pii: 2024.12.03.625240. [Epub ahead of print]
    High-throughput discovery and deep characterization of cyclin-CDK docking motifs.
    Mihkel Örd, Matthew J Winters, Mythili S Subbanna, Natalia de Martin Garrido, Victoria I Cushing, Johanna Kliche, Caroline Benz, Ylva Ivarsson, Basil J Greber, Peter M Pryciak, Norman E Davey.
      Cyclin-CDKs are master regulators of cell division. In addition to directly activating the CDK, the cyclin subunit regulates CDK specificity by binding short peptide "docking" motifs in CDK substrates. Here, we measure the relative binding strength of ∼100,000 peptides to 11 human cyclins from five cyclin families (D, E, A, B and F). Using a quantitative intracellular binding assay and large-scale tiled peptide screening, we identified a range of non-canonical binders that unveil a broader than anticipated repertoire of cyclin docking motif types. Structural and saturation mutagenesis studies revealed distinct binding modes and sequence features that govern motif recognition, binding strength, and cyclin preference. Docking motifs vary from highly selective to pan-cyclin, thereby fine-tuning the timing of CDK phosphorylation during cell cycle progression. Overall, these findings provide an unprecedented depth of understanding about the rules encoding specificity and affinity within a group of related but distinct protein domains.
    DOI:  https://doi.org/10.1101/2024.12.03.625240
  15. bioRxiv. 2024 Dec 07. pii: 2024.12.03.626727. [Epub ahead of print]
    Prediction of peptide structural conformations with AlphaFold2.
    Alexander M Ille, Christopher Markosian, Stephen K Burley, Renata Pasqualini, Wadih Arap.
      Protein structure prediction via artificial intelligence/machine learning (AI/ML) approaches has sparked substantial research interest in structural biology and adjacent disciplines. More recently, AlphaFold2 (AF2) has been adapted for the prediction of multiple structural conformations in addition to single-state structures. This novel avenue of research has focused on proteins (typically 50 residues in length or greater), while multi-conformation prediction of shorter peptides has not yet been explored in this context. Here, we report AF2-based structural conformation prediction of a total of 557 peptides (ranging in length from 10 to 40 residues) for a benchmark dataset with corresponding nuclear magnetic resonance (NMR)-determined conformational ensembles. De novo structure predictions were accompanied by structural comparison analyses to assess prediction accuracy. We found that the prediction of conformational ensembles for peptides with AF2 varied in accuracy versus NMR data, with average root-mean-square deviation (RMSD) among structured regions under 2.5 Å and average root-mean-square fluctuation (RMSF) differences under 1.5 Å. Our results reveal notable capabilities of AF2-based structural conformation prediction for peptides but also underscore the necessity for interpretation discretion.
    DOI:  https://doi.org/10.1101/2024.12.03.626727
  16. J Chem Inf Model. 2024 Dec 19.
    Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties.
    Srivathsan Badrinarayanan, Chakradhar Guntuboina, Parisa Mollaei, Amir Barati Farimani.
      Peptides are crucial in biological processes and therapeutic applications. Given their importance, advancing our ability to predict peptide properties is essential. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with graph neural networks (GNNs) to predict peptide properties. We integrate PeptideBERT, a transformer model specifically designed for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing a contrastive loss framework, Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the transformer model's predictive accuracy. Evaluations on hemolysis and nonfouling data sets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 88.057% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.
    DOI:  https://doi.org/10.1021/acs.jcim.4c01443
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