27 papers · ranked by Valyu relevance
Qiuzhen Li, Efstathios Nikolaos Vlachos, Patrick Bryant
Structure prediction technology has transformed protein design, yet key challenges remain, particularly in designing novel functions. Many proteins function through interactions with other proteins, making the rational design of these interactions a central problem. While most efforts focus on large, stable proteins…
Suzanne P. van Wier, Andrew M. Beekman
Targeting of protein-protein interactions has become of huge interest in every aspect of medicinal and biological sciences. The control of protein interactions selectively offers the opportunity to control biological processes while limiting off target effects. This interest has massively increased with the development…
Patrick Bryant, Arne Elofsson
Currently, there is no accurate method to computationally design peptide binders towards a specific protein interface using only a target structure. Experimental methods such as phage display can produce strong binders, but it is impossible to know where these bind without solving the structures. Using AlphaFold2 (AF)…
Qiuzhen Li, Efstathios Nikolaos Vlachos, Patrick Bryant
Structure prediction technology has revolutionised the field of protein design, but key questions such as how to design new functions remain. Many proteins exert their functions through interactions with other proteins, and a significant challenge is designing these interactions effectively. While most efforts have…
Sarah K Madden, Laura S Itzhaki, Skerra Arne
The process of displaying functional peptides by ‘grafting’ them onto loops of a stable protein scaffold can be used to impart binding affinity for a target, but it can be difficult to predict the affinity of the grafted peptide and the effect of grafting on scaffold stability. In this study, we show that a series of…
Jamin B. Hein, Martha S. Cyert, Polly M. Fordyce
Signal transduction pathways rely on dynamic interactions between protein globular domains and short linear motifs (SLiMs). The weak affinities of these interactions are essential to allow fast rewiring of signaling pathways and downstream responses, but pose technical challenges for interaction detection and…
Matthew P. Greving, Paul E. Belcher, Chris W. Diehnelt, Maria J. Gonzalez-Moa + 5 more
'Maria J. Gonzalez-Moa' 'Jack Emery' 'Jinglin Fu' 'Stephen Albert Johnston' 'Neal W. Woodbury' 'Vladimir N. Uversky'] Background There is a significant need for affinity reagents with high target affinity/specificity that can be developed rapidly and inexpensively. Existing affinity reagent development approaches…
Yuteng Wu, M. Teresa Bertran, Dhira Joshi, Sarah Maslen + 2 more
Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific crosslinker can require significant optimisation. We report a novel mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that…
Gergo Gogl, Boglarka Zambo, Camille Kostmann, Alexandra Cousido-Siah + 11 more
'Bastien Morlet' 'Fabien Durbesson' 'Luc Negroni' 'Pascal Eberling' 'Pau Jané' 'Yves Nominé' 'Andras Zeke' 'Søren Østergaard' 'Élodie Monsellier' 'Renaud Vincentelli' 'Gilles Travé'] Human protein networks have been widely explored but most binding affinities remain unknown, hindering quantitative interactome-function…
Shaoqing Tang, Yinuo Zhang, Pranam Chatterjee
Multi-Objective-Guided Discrete Diffusion Authors: ['Shaoqing Tang' 'Yinuo Zhang' 'Pranam Chatterjee'] Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of…
Keyu Xu, Zeyuan Di, Jianquan Zhao, Haicang Zhang + 1 more
Proteins are essential biological macromolecules that play a crucial role in living organisms. Protein-protein interactions, which govern various biological processes such as signal transduction, cell metabolism, and cell growth, are key aspect of protein function. The strength of these interactions, characterized by…
Xingyu Liu, Xinjian Ji, Christian Heinis, Jerome Waser
Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents - ethynylbenziodoxolones (EBXs)- onto peptides. These peptide-EBXs can be easily accessed, both via solution and solid phase peptide synthesis (SPPS). They can be used to couple…
Michael T. Bergman, Fiona Mukherjee, Yufan Feng, Carol K. Hall + 1 more
Solid-Binding Peptides Authors: Michael T. Bergman, Fiona Mukherjee, Yufan Feng, Carol K. Hall, Nicholas L. Abbott Solid-binding peptides (SBPs) are versatile molecules that can control a range of atomic-scale interfacial processes, but they remain challenging to discover. Current approaches for discovery rely on…
Anna Russo, Pasqualina Liana Scognamiglio, Rolando Pablo Hong Enriquez, Carlo Santambrogio + 6 more
'Rolando Pablo Hong Enriquez' 'Carlo Santambrogio' 'Rita Grandori' 'Daniela Marasco' 'Antonio Giordano' 'Giacinto Scoles' 'Sara Fortuna' 'Yang Zhang'] Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based…
Dian Chen, Y. Chen, Tong Lin, Sijie Chen + 1 more
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the inherent conformational flexibility of peptides and the limited availability of…
D’Artagnan Greene, Theodora Po, Jennifer Pan, Tanya Tabibian + 1 more
'Ray Luo'] Alzheimer's Disease (AD) is a neurodegenerative disorder that lacks effective treatment options. Anti-amyloid beta (A) antibodies are the leading drug candidates to treat AD, but the results of clinical trials have been disappointing. Introducing rational mutations into anti-A antibodies to increase their…
Wajid Arshad Abbasi, Syed Ali Abbas, Maryum Bibi, Saiqa Andleeb + 1 more
The trade-off between predictive accuracy and data availability makes it difficult to predict protein–protein binding affinity accurately. The lack of experimentally resolved protein structures limits the performance of structure-based machine learning models, which generally outperform sequence-based methods. In order…
Anil Incel, Sudhirkumar Shinde, Ignacio A. Diez, Maria M. Stollenwerk + 2 more
Immunoaffinity enrichment based on antipeptide antibodies coupled to mass spectrometry-based identification and quantification (immuno-MS) is a promising approach to translate proteomics to clinical assays with diagnostic value. This is linked to precision cancer medicine, where immuno-MS based studies of protein…
Silong Zhai, Huifeng Zhao, Jike Wang, Shaolong Lin + 6 more
Peptides mediate up to 40% of protein-protein interactions (PPIs), offering high specificity and the ability to target binding sites inaccessible to small molecules, making them promising candidates for drug development. Accurate modeling of protein-peptide complexes is crucial for understanding fundamental biological…
Hanqun Cao, Zachary Quinn, Aastha Pal, Sumi Kimura + 3 more
Protein binder design has largely optimized for affinity alone, leaving conformational selectivity unaddressed: for allosteric targets such as kinases, nuclear receptors, and GPCRs, a binder that engages both active and inactive states provides no functional specificity regardless of how tightly it binds. We introduce…
Frédéric Guyon, Gautier Moroy
Peptides are molecules involved in many essential biological activities by interacting with proteins in the body. They can also be used as therapeutic molecules, particularly to disrupt protein-protein interactions involved in disease. However, it is difficult to identify potential therapeutic peptides if the structure…
Yin Song, Xuenan Mi, Diwakar Shukla
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising candidates for drug development. However, predicting peptide-protein complexes by…
Md. Aktar Hossain, Saima Sultana
In silico analysis is a powerful technique to identify better therapeutic interventions. Molecular docking is widely used to screen ligands through analysing binding affinities for target receptors. In this study we screened ligands for two proteins which are potential drug targets: deoxyuridine triphosphate…
Angelita Rebollo, Louise Fliedel, Pierre Tuffery, Thomas R. Caulfield
In a previous study, we have shown that PEPscan can provide a cheap and rapid means to identify candidate interfering peptides (IPs), i.e., peptides able to disrupt a target protein-protein interaction. PEPscan was shown to be effective in identifying a limited number of candidate IPs specific to the target…
Authors not listed
Site-specific modifications of native-sequence proteins are technologies that underpin progresses in chemical biology, diagnostics and next-generation biotherapeutics. However, the pursuit of site-specificity has often come at the expense of scalability and usability, ultimately limiting translational potential of a…
Authors not listed
The passive membrane permeation of small-molecule drugs and relatively small hydrophobic peptides is relatively well understood. In contrast, how long polar peptides can directly pass through a membrane has remained a mystery. This process can be achieved with transcellular permeation enhancers, contributing…
Cristina Martínez-Hernández, Mariana del Carmen Aguilera-Puga, Fabien Plisson
Current cancer treatments damage healthy cells and tissues, causing short-term and long-term side effects. New treatments are desired that show greater selectivity toward cancer cells and evade the common mechanisms of multidrug resistance. Membranolytic anticancer peptides (mACPs) hold promise against cancer and…