Chemical Synthesis and Analysis

Defining short linear motif binding determinants by phage-based multiplexed deep mutational scanning

This study uses phage-based deep mutational scanning to identify binding determinants of short linear motifs between human and SARS-CoV-2 proteins, refining motifs and identifying affinity-enhancing mutations.

Single-Shot Design of a Cyclic Peptide Inhibitor of HIV-1 Membrane Fusion with EvoBind

This paper introduces EvoBind, an AI method to design cyclic peptides that inhibit HIV-1 membrane fusion, demonstrating potent inhibition of two HIV-1 strains with no toxicity.

A Plug-and-Play Platform for Automated Azapeptide Synthesis: Case study of Azapeptide-based GLP-1

This paper introduces an automated platform for azapeptide synthesis that overcomes synthetic challenges by using pre-activated building blocks and microwave-assisted synthesis, enabling efficient and scalable production of stabilized peptide therapeutics.

An mRNA Display Approach for Covalent Targeting of a Staphylococcus aureus Virulence Factor

The paper develops fluorescent probes for FphB, a Staphylococcus aureus enzyme, using mRNA display with a genetically encoded electrophile, achieving nanomolar selectivity.

De Novo Design of Peptide Masks Enables Rapid Generation of Conditionally-Active Miniprotein Binders

This paper designs de novo peptide masks to reversibly inactivate miniprotein binders, demonstrating their effectiveness in reducing EGFR antagonist binding and enabling conditional activation via stimuli like proteases or light.

Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display

This paper identifies covalent cyclic peptide inhibitors targeting protein-protein interactions using phage display, demonstrating antiviral activity against SARS-CoV-2.

Target-based de novo design of cyclic peptide binders

This paper introduces CYC_BUILDER, a reinforcement learning method for designing cyclic peptides that bind target proteins, demonstrating its effectiveness in generating potent inhibitors for TNF.

Tying the Knot: In Silico Design of Foldable Lasso Peptides

This paper designs foldable lasso peptides through sequence optimization and chemical modifications, showing improved pre-lasso stability and demonstrating cooperative benefits of cross-linking with modifications.

Exploring the effect of Hydrocarbon Cross-linkers on the Structure and Binding of Stapled p53 Peptides

This study uses simulations to analyze how hydrocarbon cross-linkers affect the structure and binding of stapled p53 peptides to MDM2, showing that longer cross-linkers increase rigidity and improve binding efficiency.

Enzyme-free biochemical production of seamlessly N-to-C cyclized peptides from natural or recombinant proteins

This paper describes a method to produce cyclic peptides from natural or recombinant proteins without enzymes, enabling cost-effective and scalable synthesis of stable, biodegradable cyclic peptides.

Peptide Information Compression Technology (PICT): A New Frontier in Therapeutic Peptide Discovery

This paper introduces PICT, a new technology for efficient therapeutic peptide discovery, and demonstrates its application in identifying active molecules with low nanomolar to micromolar potency.

Inhibition of GEF-H1-RhoA signaling in inflammation with a stapled peptide mimicry of the RhoA67-78 helix

The paper designs a stapled peptide stP5 that inhibits GEF-H1-RhoA signaling in inflammation, showing 100-fold higher activity than the unstapled P5 peptide.

Design and Biophysical Characterization of Second-Generation Cyclic Peptide LAG-3 Inhibitors for Cancer Immunotherapy

The paper designs and characterizes second-generation cyclic peptide LAG-3 inhibitors, identifying cyclic peptide 12 as the most effective with an IC50 of 4.45 µM.

Peptide therapeutic leads for multi-target inhibition of inflammatory cytokines in Inflammatory Bowel Disease - computational design and in-vitro validation

This study computationally designs and validates peptides that inhibit key inflammatory cytokines in IBD, showing reduced cytokine release in vitro.

moPPIt: De Novo Generation of Motif-Specific and Functionally Active Peptide Binders via Discrete Flow Matching

moPPIt generates motif-specific and functionally active peptide binders using sequence data, validated in vitro and in disease-relevant assays.

Peptipedia v2.0: A peptide sequence database and user-friendly web platform. A major update

Peptipedia v2.0 expands its peptide database by 45% and integrates machine learning models to annotate peptide sequences with biological activities.

Peptide generative design with weakly order-dependent autoregressive language model and lifelong learning

This paper introduces PepGenWOA, a generative model for bioactive peptide design that outperforms existing methods and enables efficient virtual screening.

Discovery of high affinity and specificity stapled peptide Bcl-xL inhibitors using bacterial surface display

The paper develops high-affinity, specific stapled peptides that inhibit Bcl-xL, showing 10 nM affinity and 100-fold selectivity over other Bcl-2 family members.

Branched multimeric peptides as affinity reagents for detection of α-Klotho protein

This paper develops branched multimeric peptides that bind α-Klotho with high affinity and selectivity, enabling its detection and labeling in biological systems.

Rapid Single-Shot Synthesis of the 217 Amino Acid-Long N-Terminal Domain of Pyocin S2

The paper synthesizes a 217 amino acid-long N-terminal domain of pyocin S2 using automated fast-flow peptide synthesis, achieving rapid production and selective uptake in Pseudomonas aeruginosa.

Discovery of reactive peptide inhibitors of human papillomavirus oncoprotein E6

The paper designs a covalent peptide inhibitor, reactide, targeting the HPV16 E6-E6AP interaction to prevent p53 degradation.

Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide

The paper develops a stapled peptide that inhibits p53-Mediator interaction, suppressing p53 transcriptional activity in cancer cells.

Head-to-tail peptide cyclization: new directions and application to urotensin II and Nrf2

The paper introduces a framework for rational head-to-tail peptide cyclization using protein structure data, demonstrating improved conformation prediction and successful application to Nrf2 and urotensin II peptides.

A designed high-affinity peptide that hijacks microtubule-based transport

The paper designs a high-affinity peptide (KinTag) that hijacks microtubule-based transport by binding KLCTPRs with nanomolar affinity, enhancing cargo transport efficiency.

Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display

This paper isolates and characterizes cyclic peptide binders using yeast surface display, showing they can bind targets like lysozyme and IL-17 with low micromolar to nanomolar affinities without chemical synthesis.

Rotamer libraries for the high-resolution design of beta-amino acid foldamers

The paper develops and validates rotamer libraries for beta3-amino acids to support their inclusion in protein design frameworks.