scholarly journals In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

2021 ◽  
Author(s):  
Junzhuo Liao ◽  
Xueqing Nie ◽  
Ilona Unarta ◽  
Spencer Ericksen ◽  
Weiping Tang
Keyword(s):  
Residence Time ◽  
Rational Design ◽  
Ternary Complex ◽  
Mechanical Energy ◽  
Protein Structures ◽  
Target Protein ◽  
Change Analysis ◽  
Bifunctional Molecules ◽  
Protein Ligands ◽  
Threshold Score

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated target protein will be escorted to the proteasome for degradation. Rational design of PROTACs require knowledge of an accurate configuration of the PROTAC induced ternary complex. This study demonstrates that native ternary poses can be distinguished by scoring candidate poses based on the pose residence time. The scoring is essentially heat-and-dissociate trials of candidate poses sampled by MD and pre-ranked by the classic MM/GBSA method. It is practical, simple to use and self-intuitive, relying on the observation that the assumed more stable native crystal ternary poses maintained a longer residence time than non-native ones at both room and higher temperatures. A time score and temperature score were generated from multiple replicate trajectories. These scores were able to correctly identify the native pose from non-native ones in all the systems examined. The absolute numbers were comparable across different systems in all currently available VHL and CRBN-containing ternary crystal structures. Therefore, it is also possible to provide an empirical criteria for unresolved ternary structures that under the conditions of this study. If a ternary pose is stable up to over a certain threshold score, it is likely a native pose. The success of the method is in part attributed to the dynamic nature of the pose change analysis which naturally involves entropic effects, one that is intrinsically unavailable with faster static scoring methods that consider molecular mechanical energy only. Protein-protein binding entropy is much more significant than in protein-ligands binding. The success is also attributed to the fact that the protein structures themselves were all stable in the short heating trials.

scholarly journals In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

2021 ◽  
Author(s):  
Junzhuo Liao ◽  
Xueqing Nie ◽  
Ilona Unarta ◽  
Spencer Ericksen ◽  
Weiping Tang
Keyword(s):  
Residence Time ◽  
Rational Design ◽  
Ternary Complex ◽  
Mechanical Energy ◽  
Protein Structures ◽  
Target Protein ◽  
Change Analysis ◽  
Bifunctional Molecules ◽  
Protein Ligands ◽  
Threshold Score

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that can induce the ubiquitination of targeted proteins via the formation of ternary complexes between an E3 ubiquitin ligase and a target protein. The poly-ubiquitinated target protein will be escorted to the proteasome for degradation. Rational design of PROTACs require knowledge of an accurate configuration of the PROTAC induced ternary complex. This study demonstrates that native ternary poses can be distinguished by scoring candidate poses based on the pose residence time. The scoring is essentially heat-and-dissociate trials of candidate poses sampled by MD and pre-ranked by the classic MM/GBSA method. It is practical, simple to use and self-intuitive, relying on the observation that the assumed more stable native crystal ternary poses maintained a longer residence time than non-native ones at both room and higher temperatures. A time score and temperature score were generated from multiple replicate trajectories. These scores were able to correctly identify the native pose from non-native ones in all the systems examined. The absolute numbers were comparable across different systems in all currently available VHL and CRBN-containing ternary crystal structures. Therefore, it is also possible to provide an empirical criteria for unresolved ternary structures that under the conditions of this study. If a ternary pose is stable up to over a certain threshold score, it is likely a native pose. The success of the method is in part attributed to the dynamic nature of the pose change analysis which naturally involves entropic effects, one that is intrinsically unavailable with faster static scoring methods that consider molecular mechanical energy only. Protein-protein binding entropy is much more significant than in protein-ligands binding. The success is also attributed to the fact that the protein structures themselves were all stable in the short heating trials.

scholarly journals Structure-Based Design of a Macrocyclic PROTAC

2019 ◽  
Author(s):  
Andrea Testa ◽  
Scott J. Hughes ◽  
Xavier Lucas ◽  
Jane E. Wright ◽  
Alessio Ciulli
Keyword(s):  
Crystal Structure ◽  
Rational Design ◽  
Ternary Complex ◽  
Enzyme Inhibitors ◽  
Cellular Activity ◽  
Chemical Probes ◽  
Bioactive Conformation ◽  
Bifunctional Molecules ◽  
Design And Synthesis ◽  
Biophysical Studies

Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Here, we report the design and synthesis of a first macrocyclic PROTAC by adding a second cyclizing linker to the BET degrader MZ1. A co-crystal structure of macroPROTAC-1 bound in a ternary complex with VHL and the second Brd4 bromodomain validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12-fold loss of binary binding affinity for Brd4, macroPROTAC-1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets.

scholarly journals Structure-Based Design of a Macrocyclic PROTAC

2019 ◽  
Author(s):  
Andrea Testa ◽  
Scott J. Hughes ◽  
Xavier Lucas ◽  
Jane E. Wright ◽  
Alessio Ciulli
Keyword(s):  
Crystal Structure ◽  
Rational Design ◽  
Ternary Complex ◽  
Enzyme Inhibitors ◽  
Cellular Activity ◽  
Chemical Probes ◽  
Bioactive Conformation ◽  
Bifunctional Molecules ◽  
Design And Synthesis ◽  
Biophysical Studies

Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Here, we report the design and synthesis of a first macrocyclic PROTAC by adding a second cyclizing linker to the BET degrader MZ1. A co-crystal structure of macroPROTAC-1 bound in a ternary complex with VHL and the second Brd4 bromodomain validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12-fold loss of binary binding affinity for Brd4, macroPROTAC-1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets.

scholarly journals In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses

2021 ◽  
Author(s):  
Junzhuo Liao ◽  
Xueqing Nie ◽  
Ilona Unarta ◽  
Spencer Ericksen ◽  
Weiping Tang
Keyword(s):  
Protein Interactions ◽  
Rational Design ◽  
Ternary Complex ◽  
Protein Protein Interactions ◽  
Dynamic Nature ◽  
Bifunctional Molecules ◽  
In Silico Modeling ◽  
Subsequent Degradation ◽  
Heating Scheme ◽  
Entropic Effects

Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce ubiquitination and subsequent degradation of proteins via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. Rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on pose occupancy time in MD, where native poses exhibit longer occupancy times than non-native ones at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by the classic MM/GBSA method. A specific heating scheme is then applied to induce ternary pose departure, generating an occupancy score and temperature score reflecting pose occupancy time and fraction. The scoring approach enables identification of the native pose in all the test systems. Beyond providing a relative rank of hypothetical poses of a given ternary system, the method could also provide empirical guidance to whether a given ternary pose is likely a native one or not. The success of the method is in part attributed to the dynamic nature of the pose departure analysis which accounts for solute entropic effects, typically neglected in the faster static pose scoring methods, while solute entropic contributions play a greater role in protein-protein interactions than in protein-ligand systems.

scholarly journals De Novo Protein Design of Photochemical Reaction Centers

2021 ◽  
Author(s):  
Nathan Ennist ◽  
Zhenyu Zhao ◽  
Steven Stayrook ◽  
Bohdana Discher ◽  
P Leslie 'Les' Dutton ◽  
...  
Keyword(s):  
Reaction Center ◽  
Charge Separation ◽  
Rational Design ◽  
De Novo ◽  
Metal Cluster ◽  
Protein Structures ◽  
Essential Elements ◽  
Reaction Centers ◽  
Transient Absorption Spectroscopy

Abstract Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families

2018 ◽  
Vol 16 (02) ◽  
pp. 1840005 ◽  
Author(s):  
Dmitry Suplatov ◽  
Yana Sharapova ◽  
Daria Timonina ◽  
Kirill Kopylov ◽  
Vytas Švedas
Keyword(s):  
Rational Design ◽  
Visual Analysis ◽  
Structural Information ◽  
Protein Structures ◽  
Web Server ◽  
Physical Contact ◽  
Protein Families ◽  
Sequence Alignments ◽  
Homologous Proteins ◽  
Correlated Mutations

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand’s binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

scholarly journals The Methionine-aromatic Motif Plays a Unique Role in Stabilizing Protein Structure

2012 ◽  
Vol 287 (42) ◽  
pp. 34979-34991 ◽  
Author(s):  
Christopher C. Valley ◽  
Alessandro Cembran ◽  
Jason D. Perlmutter ◽  
Andrew K. Lewis ◽  
Nicholas P. Labello ◽  
...  
Keyword(s):  
Rational Design ◽  
Protein Structures ◽  
Data Bank ◽  
Unique Role ◽  
Hydrophobic Residues ◽  
Receptor Complexes ◽  
Affinity Ligand ◽  
Additional Stabilization ◽  
High Affinity Ligand

Of the 20 amino acids, the precise function of methionine (Met) remains among the least well understood. To establish a determining characteristic of methionine that fundamentally differentiates it from purely hydrophobic residues, we have used in vitro cellular experiments, molecular simulations, quantum calculations, and a bioinformatics screen of the Protein Data Bank. We show that approximately one-third of all known protein structures contain an energetically stabilizing Met-aromatic motif and, remarkably, that greater than 10,000 structures contain this motif more than 10 times. Critically, we show that as compared with a purely hydrophobic interaction, the Met-aromatic motif yields an additional stabilization of 1–1.5 kcal/mol. To highlight its importance and to dissect the energetic underpinnings of this motif, we have studied two clinically relevant TNF ligand-receptor complexes, namely TRAIL-DR5 and LTα-TNFR1. In both cases, we show that the motif is necessary for high affinity ligand binding as well as function. Additionally, we highlight previously overlooked instances of the motif in several disease-related Met mutations. Our results strongly suggest that the Met-aromatic motif should be exploited in the rational design of therapeutics targeting a range of proteins.

scholarly journals Constructing synthetic-protein assemblies from de novo designed 310 helices

2021 ◽  
Author(s):  
Prasun Kumar ◽  
Neil G. Paterson ◽  
Jonathan Clayden ◽  
Derek N. Woolfson
Keyword(s):  
Rational Design ◽  
De Novo ◽  
Protein Structures ◽  
Water Soluble ◽  
Design Solution ◽  
Protein Assemblies ◽  
Synthetic Protein ◽  
Hydrophobic Cores ◽  
Α Helix ◽  
Helical Folding

Compared with the iconic α helix, 310 helices occur much less frequently in protein structures. The different 310-helical parameters lead to energetically less favourable internal energies, and a reduced tendency to pack into defined higher-order structures. Consequently, in natural proteins, 310 helices rarely extend past 6 residues, and do not form regular supersecondary, tertiary, or quaternary interactions. Here, we show that despite their absence in nature, synthetic protein-like assemblies can be built from 310 helices. We report the rational design, solution-phase characterisation, and an X-ray crystal structure for water-soluble bundles of 310 helices with consolidated hydrophobic cores. The design uses 6-residue repeats informed by analysing natural 310 helices, and incorporates aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 310-helical folding, and identify features required for stabilising assemblies in this unexplored region of protein-structure space.

scholarly journals Bifunctional Small Molecules That Mediate the Degradation of Extracellular Proteins

2020 ◽  
Author(s):  
David Caianiello ◽  
Mengwen Zhang ◽  
Jason Ray ◽  
Jake Swartzel ◽  
Emily Branham ◽  
...  
Keyword(s):  
Ubiquitin Proteasome System ◽  
Extracellular Proteins ◽  
Target Protein ◽  
Disease Treatment ◽  
Bifunctional Molecules ◽  
Synthetic Molecules ◽  
Ubiquitin Proteasome ◽  
Mode A

<p>Targeted protein degradation (TPD) has emerged as a promising and exciting therapeutic strategy. The majority of existing TPD technologies rely on the ubiquitin-proteasome system, and are therefore limited to targeting intracellular proteins. To address this limitation, we developed a class of modularly designed, bifunctional synthetic molecules called <b>MoDE-A</b>s (<b>Mo</b>lecular <b>D</b>egraders of <b>E</b>xtracellular proteins through the <b>A</b>sialoglycoprotein receptor (ASGPR)), which are capable of mediating the degradation of extracellular proteins. MoDE-A molecules mediate the formation of a ternary complex between a target protein and the ASGPR, which is expressed primarily on hepatocytes. The target protein is then endocytosed and degraded by lysosomal proteases. We demonstrated the modularity of the MoDE-A technology by synthesizing bifunctional molecules that induce the degradation of both antibody and pro-inflammatory cytokine proteins. To our knowledge, these data represent the first experimental evidence that non-proteinogenic, synthetic molecules can be employed for the TPD of extracellular proteins both <i>in vitro</i> and <i>in vivo</i>. We believe that TPD mediated by the MoDE-A technology will have widespread applications for disease treatment.</p>

scholarly journals A3D Database: Structure-based Protein Aggregation Predictions for the Human Proteome

2021 ◽  
Author(s):  
Aleksandra Elzbieta Badaczewska-Dawid ◽  
Javier Garcia-Pardo ◽  
Aleksander Kuriata ◽  
Jordi Pujols ◽  
Salvador Ventura ◽  
...  
Keyword(s):  
Protein Aggregation ◽  
Rational Design ◽  
Structural Information ◽  
Protein Solubility ◽  
Protein Structures ◽  
Human Proteome ◽  
Human Protein ◽  
Database Structure ◽  
Human Disorders ◽  
User Friendly

Motivation: Protein aggregation is associated with highly debilitating human disorders and constitutes a major bottleneck for producing therapeutic proteins. Our knowledge of the human protein structures repertoire has dramatically increased with the recent development of the AlphaFold (AF) deep-learning method. This structural information can be used to understand better protein aggregation properties and the rational design of protein solubility. This article uses the Aggrescan3D (A3D) tool to compute the structure-based aggregation predictions for the human proteome and make the predictions available in a database form. Results: Here, we present the A3D Database, in which we analyze the AF-predicted human protein structures (for over 17 thousand non-membrane proteins) in terms of their aggregation properties using the A3D tool. Each entry of the A3D Database provides a detailed analysis of the structure-based aggregation propensity computed with A3D. The A3D Database implements simple but useful graphical tools for visualizing and interpreting protein structure datasets. We discuss case studies illustrating how the database could be used to analyze physiologically relevant proteins. Furthermore, the database enables testing the influence of user-selected mutations on protein solubility and stability, all integrated into a user-friendly interface. Availability and implementation: A3D Database is freely available at: http://biocomp.chem.uw.edu.pl/A3D2/hproteome

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