Protein-protein Interaction Surfaces Research Articles

Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold

For mitogen-activated protein kinases (MAPKs) a shallow surface—distinct from the substrate binding pocket—called the D(ocking)-groove governs partner protein binding. Screening of broad range of Michael acceptor compounds identified a double-activated, sterically crowded cyclohexenone moiety as a promising scaffold. We show that compounds bearing this structurally complex chiral warhead are able to target the conserved MAPK D-groove cysteine via reversible covalent modification and interfere with the protein-protein interactions of MAPKs. The electronic and steric properties of the Michael acceptor can be tailored via different substitution patterns. The inversion of the chiral center of the warhead can reroute chemical bond formation with the targeted cysteine towards the neighboring, but less nucleophilic histidine. Compounds bind to the shallow MAPK D-groove with low micromolar affinity in vitro and perturb MAPK signaling networks in the cell. This class of chiral, cyclic and enhanced 3D shaped Michael acceptor scaffolds offers an alternative to conventional ATP-competitive drugs modulating MAPK signaling pathways.

Structural evidence for protein-protein interaction between the non-canonical methyl-CpG-binding domain of SETDB proteins and C11orf46

SETDB1 and SETDB2 mediate trimethylation of histone H3 lysine 9 (H3K9), an epigenetic hallmark of repressive chromatin. They contain a non-canonical methyl-CpG-binding domain (MBD) and bifurcated SET domain, implying interplay between H3K9 trimethylation and DNA methylation in SETDB functions. Here, we report the crystal structure of human SETDB2 MBD bound to the cysteine-rich domain of a zinc-binding protein, C11orf46. SETDB2 MBD comprises the conserved MBD core and a unique N-terminal extension. Although the MBD core has the conserved basic concave surface for DNA binding, it utilizes it for recognition of the cysteine-rich domain of C11orf46. This interaction involves the conserved arginine finger motif and the unique N-terminal extension of SETDB2 MBD, with a contribution from intermolecular β-sheet formation. Thus, the non-canonical MBD of SETDB1/2 seems to have lost methylated DNA-binding ability but gained a protein-protein interaction surface. Our findings provide insight into the molecular assembly of SETDB-associated repression complexes.

AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics.

Peptides have attracted much attention recently owing to their well-balanced properties as drugs against protein-protein interaction (PPI) surfaces. Molecular simulation-based predictions of binding sites and amino acid residues with high affinity to PPI surfaces are expected to accelerate the design of peptide drugs. Mixed-solvent molecular dynamics (MSMD), which adds probe molecules or fragments of functional groups as solutes to the hydration model, detects the binding hotspots and cryptic sites induced by small molecules. The detection results vary depending on the type of probe molecule; thus, they provide important information for drug design. For rational peptide drug design using MSMD, we proposed MSMD with amino acid residue probes, named amino acid probe-based MSMD (AAp-MSMD), to detect hotspots and identify favorable amino acid types on protein surfaces to which peptide drugs bind. We assessed our method in terms of hotspot detection at the amino acid probe level and binding free energy prediction with amino acid probes at the PPI site for the complex structure that formed the PPI. In hotspot detection, the max-spatial probability distribution map (max-PMAP) obtained from AAp-MSMD detected the PPI site, to which each type of amino acid can bind favorably. In the binding free energy prediction using amino acid probes, ΔGFE obtained from AAp-MSMD roughly estimated the experimental binding affinities from the structure-activity relationship. AAp-MSMD, with amino acid probes, provides estimated binding sites and favorable amino acid types at the PPI site of a target protein.

Persistent Degradation of HER2 Protein by Hybrid nanoPROTAC for Programmed Cell Death.

Proteolysis-targeting chimera (PROTAC) has emerged as a promising strategy for degrading proteins of interest. Peptide-based PROTACs offer several advantages over small-molecule-based PROTACs, such as high specificity, low toxicity, and large protein-protein interaction surfaces. However, peptide-based PROTACs have several intrinsic shortcomings that strongly limit their application including poor cell permeability and low stability and potency. Herein, we designed a nanosized hybrid PROTAC (GNCTACs) to target and degrade human epidermal growth factor receptor 2 (HER2) in tumor cells. Gold nanoclusters (GNCs) were utilized to connect HER2-targeting peptides and cereblon (CRBN)-targeting ligands. GNCTACs could overcome the intrinsic barriers of peptide-based PROTACs, efficiently delivering HER2-targeting peptides in the cytoplasm and protecting them from degradation. Furthermore, a fasting-mimicking diet was applied to enhance the cellular uptake and proteasome activity. Consequently, more than 95% of HER2 in SKBR3 cells was degraded by GNCTACs, and the degradation lasted for at least 72 h, showing a catalytic-like reaction.

Mobile genetic element-encoded putative DNA primases composed of A-family polymerase-SSB pairs.

Mobile genetic elements can encode a wide variety of genes that support their own stability and mobility as well as genes that provide accessory functions to their hosts. Such genes can be adopted from host chromosomes and can be exchanged with other mobile elements. Due to their accessory nature, the evolutionary trajectories of these genes can differ from those of essential host genes. The mobilome therefore provides a rich source of genetic innovation. We previously described a new type of primase encoded by S. aureus SCCmec elements that is composed of an A-family polymerase catalytic domain in complex with a small second protein that confers single-stranded DNA binding. Here we use new structure prediction methods in conjunction with sequence database searches to show that related primases are widespread among putative mobile genetic elements in the Bacillota. Structure predictions show that the second protein adopts an OB fold (common among single-stranded DNA binding (SSB) proteins) and these predictions were far more powerful than simple sequence comparisons in identifying its homologs. The protein-protein interaction surface varies among these polymerase-SSB complexes appear to have arisen repeatedly by exploiting partial truncations of the polymerase's N-terminal accessory domains.

Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.

Driving mechanisms of many biological functions in a cell include physical interactions of proteins. As protein-protein interactions (PPIs) are also important in disease development, protein-protein interactions are highlighted in the pharmaceutical industry as possible therapeutic targets in recent years. To understand the variety of protein-protein interactions in a proteome, it is essential to establish a method that can identify similarity and dissimilarity between protein-protein interactions for inferring the binding of similar molecules, including drugs and other proteins. In this study, we developed a novel method, protein-protein interaction-Surfer, which compares and quantifies similarity of local surface regions of protein-protein interactions. protein-protein interaction-Surfer represents a protein-protein interaction surface with overlapping surface patches, each of which is described with a three-dimensional Zernike descriptor (3DZD), a compact mathematical representation of 3D function. 3DZD captures both the 3D shape and physicochemical properties of the protein surface. The performance of protein-protein interaction-Surfer was benchmarked on datasets of protein-protein interactions, where we were able to show that protein-protein interaction-Surfer finds similar potential drug binding regions that do not share sequence and structure similarity. protein-protein interaction-Surfer is available at https://kiharalab.org/ppi-surfer.

Discovery of Novel Small Molecule Inhibitors Disrupting the PCSK9-LDLR Interaction.

Proprotein convertase subtilisin kexin 9 (PCSK9) has been identified as a reliable therapeutic target for hypercholesterolemia and coronary artery heart diseases since the monoclonal antibodies of PCSK9 have launched. Disrupting the protein-protein interaction (PPI) between PCSK9 and the low-density lipoprotein receptor (LDLR) has been considered as a promising approach for developing PCSK9 inhibitors. However, PPIs have been traditionally considered difficult to target by small molecules since the PPI surface is usually large, flat, featureless, and without a "pocket" or "groove" for ligand binding. The PCSK9-LDLR PPI interface is such a typical case. In this study, a potential binding pocket was generated on the PCSK9-LDLR PPI surface of PCSK9 through induced-fit docking. On the basis of this induced binding pocket, virtual screening, molecular dynamics (MD) simulation, and biological evaluations have been applied for the identification of novel small molecule inhibitors of PCSK9-LDLR PPI. Among the selected compounds, compound 13 exhibited certain PCSK9-LDLR PPI inhibitory activity (IC50: 7.57 ± 1.40 μM). The direct binding affinity between 13 and PCSK9 was determined with a KD value of 2.50 ± 0.73 μM. The LDLR uptake function could be also restored to a certain extent by 13 in HepG2 cells. This well-characterized hit compound will facilitate the further development of novel small molecule inhibitors of PCSK9-LDLR PPI.

Abstract 2471: IDP-121, a first in class staple peptide targeting c-MYC

Abstract MYC is a transcription factor involved in fundamental cellular functions such as proliferation, apoptosis, differentiation, metabolism and, as lately discovered, immune response. [1,2] It is deregulated in a wide variety of aggressive human cancers and its overexpression is one of the most common events associated with tumorigenesis, making it one of the most attractive yet challenging targets in oncology.[3] c-MYC protein structure is mostly disordered in its monomeric state, and assumes a helix-loop-helix fold upon binding to its protein partner MAX. The absence of clefts or hydrophobic pockets (typical of enzymes) and the large protein-protein interaction surface formed in the c-MYC/MAX complex represent a challenge for the design of small molecule inhibitors. Moreover, the intra-nuclear localization of c-MYC renders the use of antibodies impossible. Hence, it is not surprising that conventional drug development has failed and no therapeutic has yet progressed into clinical trials.[4] Here we describe IDP-121, a stapled peptide specifically designed to target c-MYC protein. A library based on c, l, n-MYC and MAX druggable regions was designed, with a bias towards disruption of c-MYC (residual) intra-protein interactions. The primary goal in the initial screen was to identify compounds able to block c-MYC's fold-like state that allows binding to MAX. A functional (cellular) assay was used for our screening program to ensure cell and nuclear penetration. Stapling technology was implemented to overcome the lack of stability and cell permeability common to unmodified peptides, whilst retaining c-MYC specificity and a large surface coverage. The lead compound, IDP-121, is stable to proteolysis and is rapidly internalized into cells, distributing efficiently into the nucleus (see Abstract 3). The interaction with c-MYC was characterized by HSQC-NMR, Fluorescence Polarization (FP) and Surface Plasmon Resonance (SPR). IDP-121 binds specifically to c-MYC, with a Kd of 400 nM, an affinity ten-fold higher than c-MYC/MAX interaction, allowing IDP-121 to displace MAX from the binding site. SAR studies were conducted to tailor the elements essential for its biological function. Isolated protein complex (ELISA), and pull-down and FRET experiments confirmed disruption of the c-MYC/MAX complex by IDP-121 (see Abstracts 2). The drug-like properties and efficacy in hematological and solid tumors of IDP-121 have been demonstrated in vivo (see Abstracts 2 and 3). In addition, IDP-121 has progressed through GLP toxicology studies without evidence of major systemic toxicity, allowing for the first viable Myc-targeted therapy to enter Phase 1 clinical trials in 2021. 1.Casey S.C. et al. Science 2016; 352 (6282): 227–231 2.Casey S.C. et al. Blood 2018; 131 (18): 2007-20153.Dang CV. Cell. 2012;149(1):22-35.4. Whitfield J. R., Front. Cell Dev. Biol. 2017 Citation Format: Carmen Calvis, Andreas Beier, Michael Feichtinger, Theresa Höfurthner, Miguel Moreno, Ramon Messeguer, Robert Konrat, Santiago Esteban, Laura Nevola. IDP-121, a first in class staple peptide targeting c-MYC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2471.

Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS).

Formulation of protein-based therapeutics employ advanced formulation and analytical technologies for screening various parameters such as buffer, pH, and excipients. At a molecular level, physico-chemical properties of a protein formulation depend on self-interaction between protein molecules, protein-solvent and protein-excipient interactions. This work describes a novel in silico approach, SILCS-Biologics, for structure-based modeling of protein formulations. SILCS Biologics is based on the Site-Identification by Ligand Competitive Saturation (SILCS) technology and enables modeling of interactions among different components of a formulation at an atomistic level while accounting for protein flexibility. It predicts potential hotspot regions on the protein surface for protein-protein and protein-excipient interactions. Here we apply SILCS-Biologics on a Fab domain of a monoclonal antibody (mAbN) to model Fab-Fab interactions and interactions with three amino acid excipients, namely, arginine HCl, proline and lysine HCl. Experiments on 100mg/ml formulations of mAbN showed that arginine increased, lysine reduced, and proline did not impact viscosity. We use SILCS-Biologics modeling to explore a structure-based hypothesis for the viscosity modulating effect of these excipients. Current efforts are aimed at further validation of this novel computational framework and expanding the scope to model full mAb and other protein therapeutics.

In Vivo Reporter System for miRNA-Mediated RNA Silencing.

Argonaute proteins play a central role in the evolutionarily conserved mechanisms of RNA silencing. Programmed by a variety of small RNAs, including miRNAs, they recognize their target nucleic acids and modulate gene expression by various means. Argonaute proteins are large complex molecules. Therefore, to better understand the mechanisms they use to regulate gene expression, it is necessary to identify regions of them bearing functional importance (protein-protein interaction surfaces, acceptor sites of posttranslational modifications, etc.). Identification of these regions can be performed using a variety of mutant screens. Here we describe a transient reporter assay system, which is suitable to carry out rapid functional assessment of mutant Argonaute molecules before proceeding to their more detailed biochemical characterization.

Protein-protein interactions: a structural view of inhibition strategies and the IL-23/IL-17 axis.

Protein-protein interactions are central to biology and provide opportunities to modulate disease with small-molecule or protein therapeutics. Recent developments in the understanding of the tractability of protein-protein interactions are discussed with a focus on the ligandable nature of protein-protein interaction surfaces. General principles of inhibiting protein-protein interactions are illustrated with structural biology examples from six members of the IL-23/IL-17 signaling family (IL-1, IL-6, IL-17, IL-23 RORγT and TNFα). These examples illustrate the different approaches to discover protein-protein interaction inhibitors on a target-specific basis that has proven fruitful in terms of discovering both small molecule and biologic based protein-protein interaction inhibitors.

Abstract LB-A11: Quantitative and qualitative characterization of spontaneous resistance to targeted protein degradation

Abstract Targeted protein degradation (TPD) by heterobifunctional small molecules commonly called PROTACs has recently emerged as a promising novel strategy in drug development. PROTACs hijack the endogenous cellular degradation machinery by recruiting E3 ubiquitin ligases to a protein of interest, resulting in its ubiquitination and degradation by the proteasome. The first two PROTACs have entered clinical investigation this year, but resistance mechanisms to this novel pharmacology are not yet thoroughly understood. Here, we set out to systematically quantify and characterize spontaneous resistance to TPD. For this, we made use of the well-characterized PROTACs dBET6 and ARV-771, that induce degradation of BET bromodomain proteins by recruitment of the E3 ligase CRBN or VHL, respectively. We estimated spontaneous resistance rates by exposing cells to lethal doses of drug and monitoring for the emergence of resistant clones. We detected important quantitative differences between the two PROTACs, with resistance rates to the VHL-based degrader ARV-771 being significantly lower than to dBET6. To characterize the mechanism of resistance, we implemented a customized hybrid-capture sequencing pipeline for known determinants of PROTAC sensitivity and applied it to drug-resistant cells, revealing several resistance-conferring mutations. Mapping of the mutations on crystal structures of the E3 ligase complexes highlighted their clustering at the drug binding pocket, as well as on important protein-protein interaction surfaces in the complex. The majority of identified mutations affected the hijiacked E3 ligase complex directly and not the general ubiquitination machinery, thereby not conferring cross-resistance to different PROTACS. This suggests combination treatment with degraders that exploit different E3 ligases as a viable strategy to limit emergence of PROTAC resistance. Citation Format: Matthias Brand, Georg E. Winter. Quantitative and qualitative characterization of spontaneous resistance to targeted protein degradation [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-A11. doi:10.1158/1535-7163.TARG-19-LB-A11

DUF3669, a \u201cdomain of unknown function\u201d within ZNF746 and ZNF777, oligomerizes and contributes to transcriptional repression

BackgroundZNF746 and ZNF777 belong to a subset of the large Krüppel-associated box (KRAB) zinc finger (ZNF) transcription factor family. They contain, like four other members in human, an additional conserved domain, the “domain of unknown function 3669” (DUF3669). Previous work on members of this subfamily suggested involvement in transcriptional regulation and aberrant ZNF746 overexpression leads to neuronal cell death in Parkinson’s disease.ResultsHere we demonstrate that N-terminal protein segments of the ZNF746a major isoform and ZNF777 act in concert to exert moderate transcriptional repression activities. Full potency depended on the intact configuration consisting of DUF3669, a variant KRAB domain and adjacent sequences. While DUF3669 contributes an intrinsic weak inhibitory activity, the isolated KRAB-AB domains did not repress. Importantly, DUF3669 provides a novel protein-protein interaction interface and mediates direct physical interaction between the members of the subfamily in oligomers. The ZNF746 protein segment encoded by exons 5 and 6 boosted repressor potency, potentially due to the presence of an acceptor lysine for sumoylation at K189. Repressor activity of the potent canonical ZNF10 KRAB domain was not augmented by heterologous transfer of DUF3669, pointing to the importance of context for DUF3669’s impact on transcription. Neither ZNF746a nor ZNF777 protein segments stably associated with TRIM28 within cells. Isoform ZNF746b that contains, unlike the major isoform, a full-length KRAB-A subdomain, displayed substantially increased repressor potency. This increase is due to canonical mechanisms known for KRAB domains since it did not take place in HAP1 knockout models of TRIM28 and SETDB1. A glycine to glutamic acid replacement that complies with a bona fide conserved “MLE” sequence within KRAB-A led to a further strong gain in repressor potency to levels comparable to those of the canonical ZNF10 KRAB domain. Each gain of repressive activity was accompanied by an enhanced interaction with TRIM28 protein.ConclusionDUF3669 adds a protein-protein interaction surface to a subgroup of KRAB-ZNF proteins within an N-terminal configuration with variant KRAB and adjacent sequences likely regulated by sumoylation. DUF3669 contributes to transcriptional repression strength and its homo- and hetero-oligomerization characteristics probably extended the regulatory repertoire of KRAB-ZNF transcription factors during amniote evolution.

Refining the Quality of Monoclonal Antibodies: Grafting Unique Peptide-Binding Site in the Fab Framework.

Monoclonal antibodies (mAbs) are a major therapeutic modality. Grafting the meditope binding site onto mAbs, also known as meditope-enabling, can extend the usefulness of mAbs by providing an additional protein-protein interaction surface without altering the stability or antigen binding. We have previously used this site for attaching dyes, cytotoxic drugs, and entire proteins. Here, we provide a simple protocol for meditope-enabling mAbs, and verifying meditope and antigen binding using flow cytometry (FACS).

RNA Display Methods for the Discovery of Bioactive Macrocycles.

The past two decades have witnessed the emergence of macrocycles, including macrocyclic peptides, as a promising yet underexploited class of de novo drug candidates. Both rational/computational design and in vitro display systems have contributed tremendously to the development of cyclic peptide binders of either traditional targets such as cell-surface receptors and enzymes or challenging targets such as protein-protein interaction surfaces. mRNA display, a key platform technology for the discovery of cyclic peptide ligands, has become one of the leading strategies that can generate natural-product-like macrocyclic peptide binders with antibody-like affinities. On the basis of the original cell-free transcription/translation system, mRNA display is highly evolvable to realize its full potential by applying genetic reprogramming and chemical/enzymatic modifications. In addition, mRNA display also allows the follow-up hit-to-lead development using high-throughput focused affinity maturation. Finally, mRNA-displayed peptides can be readily engineered to create chemical conjugates based on known small molecules or biologics. This review covers the birth and growth of mRNA display and discusses the above features of mRNA display with success stories and future perspectives and is up to date as of August 2018.

A Short BRCA2-Derived Cell-Penetrating Peptide Targets RAD51 Function and Confers Hypersensitivity toward PARP Inhibition.

Under conditions of genotoxic stress, cancer cells strongly rely on efficient DNA repair to survive and proliferate. The human BRCA2 tumor suppressor protein is indispensable for the repair of DNA double-strand breaks by homologous recombination (HR) by virtue of its ability to promote RAD51 loading onto single-stranded DNA. Therefore, blocking the interaction between BRCA2 and RAD51 could significantly improve the efficacy of conventional anticancer therapies. However, targeting protein-protein interaction (PPI) interfaces has proven challenging because flat and large PPI surfaces generally do not support binding of small-molecule inhibitors. In contrast, peptides are more potent for targeting PPIs but are otherwise difficult to deliver into cells. Here, we report that a synthetic 16-mer peptide derived from the BRC4 repeat motif of BRCA2 is capable of blocking RAD51 binding to BRCA2. Efficient noncytotoxic cellular uptake of a nona-arginine (R9)-conjugated version of the BRC4 peptide interferes with DNA damage-induced RAD51 foci formation and HR. Moreover, transduction of the BRC4 peptide impairs replication fork-protective function of BRCA2 and triggers MRE11-dependent degradation of nascent DNA in response to DNA replication stress. Finally, the BRC4 cell-penetrating peptide (CPP) confers selective hypersensitivity to PARP inhibition in cancer cells but spares noncancerous cells. Taken together, our data highlight an innovative approach to develop novel peptide-based DNA repair inhibitors and establish BRCA2-derived CPPs as promising anticancer agents. Mol Cancer Ther; 17(7); 1392-404. ©2018 AACR.

Disrupting a key hydrophobic pair in the oligomerization interface of the actinoporins impairs their pore-forming activity.

Crystallographic data of the dimeric and octameric forms of fragaceatoxin C (FraC) suggested the key role of a small hydrophobic protein-protein interaction surface for actinoporins oligomerization and pore formation in membranes. However, site-directed mutagenesis studies supporting this hypothesis for others actinoporins are still lacking. Here, we demonstrate that disrupting the key hydrophobic interaction between V60 and F163 (FraC numbering scheme) in the oligomerization interface of FraC, equinatoxin II (EqtII), and sticholysin II (StII) impairs the pore formation activity of these proteins. Our results allow for the extension of the importance of FraC protein-protein interactions in the stabilization of the oligomeric intermediates of StII and EqtII pointing out that all of these proteins follow a similar pathway of membrane disruption. These findings support the hybrid pore proposal as the universal model of actinoporins pore formation. Moreover, we reinforce the relevance of dimer formation, which appears to be a functional intermediate in the assembly pathway of some different pore-forming proteins.

Virtual Screening in Search of Allosteric Modulators of Nav1.1 Channels

Voltage-gated Na+ (Nav) channels provide the basis for neuronal excitability in the brain. Of the nine Nav channel isoforms (Nav1.1-Nav1.9), Nav1.1 exhibits cell-specific distribution in fast-spiking parvalbumin (PV) interneurons in the cortical circuit. Reduced function of PV interneurons results in impairment of the cognitive domain, a bio-signature common to a variety of neuropsychiatric disorders. Thus, selective allosteric modulators targeting Nav1.1 might provide new means to rescue PV interneuron function and improve cognition. Previous studies have identified fibroblast growth factor 14 (FGF14) as a functionally relevant regulator of Nav1.1 channels. Binding of FGF14 to the Nav1.1 C-terminal tail results in modulation of Nav1.1-mediated peak transient currents and biophysical properties of the channel activation and steady-state inactivation. The FGF14:Nav1.1 protein:protein interaction (PPI) interface might therefore provide a novel target for the development of Nav1.1 allosteric modulators.In search of small molecules targeting Nav1.1, we conducted a ligand-based high-throughput virtual screening using a FGF14:Nav1.1 homology model based on available crystal structures of homologous proteins. The UCSF chimera software was used to determine the region of interaction between FGF14 and Nav1.1, and Autodock was used to create a grid box surrounding this area to identify critical amino acids at the PPI surface of FGF14.This region of interest was submitted to the Texas Advanced Computing Center (TACC) drug discovery database, which identified 1001 ZINC compounds out of 642,759 possible ligands against the interaction site. Scores ranged from −13 to 0, with lower scores indicating greater likelihood of binding to the FGF14 surface, and thus interfering with Nav 1.1 binding. On-going counter and orthogonal screenings using in heterologous systems as well as Schrodinger Advanced Drug Discovery Suite are being used to provide in-cell validation of 14 identified hits and understanding of the target-ligand interactions. These small molecules might represent a new class of PPI-based Nav1.1-specific allosteric modulators with applicability as cognitive enhancers.

Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria.

Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe2+, Fe3+, and S2- ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture.

JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures.

The database JET2 Viewer, openly accessible at http://www.jet2viewer.upmc.fr/, reports putative protein binding sites for all three-dimensional (3D) structures available in the Protein Data Bank (PDB). This knowledge base was generated by applying the computational method JET2 at large-scale on more than 20 000 chains. JET2 strategy yields very precise predictions of interacting surfaces and unravels their evolutionary process and complexity. JET2 Viewer provides an online intelligent display, including interactive 3D visualization of the binding sites mapped onto PDB structures and suitable files recording JET2 analyses. Predictions were evaluated on more than 15 000 experimentally characterized protein interfaces. This is, to our knowledge, the largest evaluation of a protein binding site prediction method. The overall performance of JET2 on all interfaces are: Sen = 52.52, PPV = 51.24, Spe = 80.05, Acc = 75.89. The data can be used to foster new strategies for protein-protein interactions modulation and interaction surface redesign.