Structure-Based Stabilization of Non-native Protein–Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design

Protein−protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein−protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots.

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Engineering cell signaling modulators from native protein–protein interactions

Current Opinion in Structural Biology ◽

10.1016/j.sbi.2016.11.002 ◽

2017 ◽

Vol 45 ◽

pp. 25-35 ◽

Cited By ~ 8

Author(s):

Wei Zhang ◽

Moshe Ben-David ◽

Sachdev S Sidhu

Keyword(s):

Cell Signaling ◽

Protein Interactions ◽

Native Protein ◽

Protein Protein Interactions

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Study of intra–inter species protein–protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11

In Silico Pharmacology ◽

10.1007/s40203-017-0021-5 ◽

2017 ◽

Vol 5 (1) ◽

Cited By ~ 5

Author(s):

Shakhinur Islam Mondal ◽

Zabed Mahmud ◽

Montasir Elahi ◽

Arzuba Akter ◽

Nurnabi Azad Jewel ◽

...

Keyword(s):

Escherichia Coli ◽

Drug Design ◽

Protein Interactions ◽

Drug Targets ◽

Potential Drug ◽

Protein Protein Interactions ◽

Potential Drug Targets

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Synthesis of Epitope-Targeting Antibody Based on Native Protein–Protein Interactions for Ftsz Filamentation Suppressor

10.21203/rs.3.rs-757826/v1 ◽

2021 ◽

Author(s):

Hikaru Nakazawa ◽

Taiji Katsuki ◽

Takashi Matsui ◽

Atsushi Tsugita ◽

Takeshi Yokoyama ◽

...

Keyword(s):

Molecular Evolution ◽

Phage Display ◽

Protein Interactions ◽

Selection Process ◽

Evolutionary Engineering ◽

Temperature Sensitive ◽

Native Protein ◽

Protein Protein Interactions ◽

Division Rate ◽

Evolution Approach

Abstract Phage display and biopanning is a powerful tool for generating binding molecules for a specific target. However, the selection process based on binding affinity provides no assurance for the antibody’s affinity to the target epitope. In this study, we propose a molecular-evolution approach guided by native protein–protein interactions to generate epitope-targeting antibodies. The binding-site sequence in a native protein was grafted into a complementarity-determining region (CDR) in the antibody, and a nonrelated CDR loop (in the grafted antibody) was randomized by phage display techniques. In this construction of antibodies by integrating graft and evolution technology (CAnIGET method), suitable grafting of the functional sequence weakly functionalized the antibody, and the molecular-evolution approach enhanced the binding function to inhibit the native protein–protein interactions. Antibody fragments with an affinity for filamenting temperature-sensitive mutant Z (FtsZ) were constructed and completely inhibited the polymerization of FtsZ. Consequently, the expression of these fragments drastically decreased the cell division rate. We demonstrate the potential of the CAnIGET method with the use of native protein–protein interactions for steady epitope-specific evolutionary engineering.

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Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs

10.1101/241810 ◽

2018 ◽

Cited By ~ 1

Author(s):

Zhen-lu Li ◽

Matthias Buck

Keyword(s):

Electrostatic Interaction ◽

Protein Interactions ◽

Protein Complex ◽

Complex Structure ◽

Md Simulations ◽

Potential Functions ◽

Amino Acid Side Chain ◽

Native Protein ◽

Protein Protein Interactions ◽

Steering Mechanism

ABSTRACTNative protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we investigate the association of the SAM domains of the EphA2 receptor and SHIP2 enzyme by performing a combined total of 48 μs all-atom molecular dynamics (MD) simulations. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% and to 18.3% by scaling the vdW solute-solvent interactions (better fitting the solvation free energy of amino acid side chain analogues) and by an increase of vdW radius of guanidinium interactions, and thus a dramatic reduction of electrostatic interaction between Arg and Glu/Asn in CHARMM36m, respectively. These modifications effectively improve the overly sticky association of proteins, such as ubiquitin, using the original potential function. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a pre-orientation guided by electrostatic interaction, consistent with an electrostatic steering mechanism. The complex could then transform to the native protein interaction surfaces directly from a well pre-orientated position (Δinterface-RMSD < 5Å). In other cases, modest (< 90°) orientational and/or translational adjustments are needed (5 Å <Δi-RMSD <10 Å) to the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a re-association to the correct complex structure is still rare. Instead a most non-native complexes are undergoing configurational changes/surface searching, which do not lead to native structures on a timescale of 250 ns. These observations provide a rich picture on mechanisms of protein-protein complex formation, and suggest that computational predictions of native complex protein-protein interactions could be improved further.

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Spatial and temporal control of norovirus protease activity is determined by polyprotein processing and intermolecular interactions within the viral replication complex

10.1101/175463 ◽

2017 ◽

Cited By ~ 2

Author(s):

Edward Emmott ◽

Alexis de Rougemont ◽

Jürgen Haas ◽

Ian Goodfellow

Keyword(s):

Viral Replication ◽

Protein Interactions ◽

Full Range ◽

Antiviral Drug ◽

Viral Gastroenteritis ◽

Protein Protein Interactions ◽

Replication Complex ◽

Viral Replication Complex ◽

Stable Forms

AbstractNorovirus infections are a major cause of acute viral gastroenteritis and a significant burden to human health globally. A vital process for norovirus replication is the processing of the nonstructural polyprotein, by an internal protease, into the necessary viral components required to form the viral replication complex. This cleavage occurs at different rates resulting in the accumulation of stable precursor forms. In this report, we characterized how precursor forms of the norovirus protease accumulate during infection. Using stable forms of the protease precursors we demonstrated that these are all proteolytically activein vitro, but that when expressed in cells, activity is determined by both substrate and protease localization. Whilst all precursors could cleave a replication complex-associated substrate, only a subset of precursors lacking NS4 were capable of efficiently cleaving a cytoplasmic substrate. For the first time, the full range of protein-protein interactions between murine and human norovirus proteins were mapped by LUMIER assay, with conserved interactions between replication complex members, modifying the localization of a subset of precursors. Finally, we demonstrate that re-targeting of a poorly cleaved artificial cytoplasmic substrate to the replication complex is sufficient to permit efficient cleavage in the context of norovirus infection. This offers a model for how norovirus can regulate the timing of substrate cleavage throughout the replication cycle. The norovirus protease represents a key target in the search for effective antiviral treatments for norovirus infection. An improved understanding of protease function and regulation, as well as identification of interactions between the other non-structural proteins, offers new avenues for antiviral drug design.

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26th Annual GP2A Medicinal Chemistry Conference & 32nd Journées Franco-Belges de Pharmacochimie

Pharmaceuticals ◽

10.3390/ph12020073 ◽

2019 ◽

Vol 12 (2) ◽

pp. 73

Author(s):

Patrick Dallemagne ◽

Christophe Rochais ◽

Pascal Marchand ◽

Thierry Besson

Keyword(s):

Drug Design ◽

Natural Product ◽

Protein Interactions ◽

Medicinal Chemistry ◽

Young Researcher ◽

Protein Protein Interactions ◽

Computer Aided Drug Design ◽

Computer Aided ◽

Wide Group ◽

New Strategies

As a joint meeting, the 26th Medicinal Chemistry Conference of GP2A and 32nd Journées Franco-Belges de Pharmacochimie took place between 13th and 15th June at Asnelles sur Mer (Normandie, France), providing a unique opportunity for a wide group of European medicinal chemists to engage. Topics included chemical tools for medicinal chemistry, protein-protein interactions, epigenetics, natural product-inspired molecules, computer-aided drug design, and new strategies for the design and development of drugs. Abstracts of invited lectures, proffered young researcher communications, flash communications and posters presented during the meeting are collected in this report.

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