Protein-protein interactions are considered as one of the next generation of therapeutic targets. Specific tools thus need to be developed to tackle this challenging chemical space. In an effort to ...derive some common principles from recent successes, we have built 2P2Idb (freely accessible at http://2p2idb.cnrs-mrs.fr), a hand-curated structural database dedicated to protein-protein interactions with known orthosteric modulators. It includes all interactions for which both the protein-protein and protein-ligand complexes have been structurally characterized. A web server provides links to related sites of interest, binding affinity data, pre-calculated structural information about protein-protein interfaces and 3D interactive views through java applets. Comparison of interfaces in 2P2Idb to those of representative datasets of heterodimeric complexes has led to the identification of geometrical parameters and residue properties to assess the druggability of protein-protein complexes. A tool is proposed to calculate a series of biophysical and geometrical parameters that characterize protein-protein interfaces. A large range of descriptors are computed including, buried accessible surface area, gap volume, non-bonded contacts, hydrogen-bonds, atom and residue composition, number of segments and secondary structure contribution. All together the 2P2I database represents a structural source of information for scientists from academic institutions or pharmaceutical industries.
Protein–protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next ...generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse “PPI-like” modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein–protein interfaces with distinct “druggability” potential using homogeneous time-resolved fluorescence (HTRF) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries. This observation correlates with the predicted “druggability” of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined “druggable” bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets.
Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which ...localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L ...protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication. Transcription of the six genes occurs sequentially. This implies ending and re-initiating mRNA synthesis at each intergenic region (IGR). We explored here to which extent the binding of the X domain of P (XD) to the C-terminal region of the N protein (N.sub.TAIL) is involved in maintaining the P/L complex anchored to the nucleocapsid template during the sequential transcription. Amino acid substitutions introduced in the XD-binding site on N.sub.TAIL resulted in a wide range of binding affinities as determined by combining protein complementation assays in E. coli and human cells and isothermal titration calorimetry. Molecular dynamics simulations revealed that XD binding to N.sub.TAIL involves a complex network of hydrogen bonds, the disruption of which by two individual amino acid substitutions markedly reduced the binding affinity. Using a newly designed, highly sensitive dual-luciferase reporter minigenome assay, the efficiency of re-initiation through the five measles virus IGRs was found to correlate with N.sub.TAIL /XD K.sub.D . Correlatively, P transcript accumulation rate and F/N transcript ratios from recombinant viruses expressing N variants were also found to correlate with the N.sub.TAIL to XD binding strength. Altogether, our data support a key role for XD binding to N.sub.TAIL in maintaining proper anchor of the P/L complex thereby ensuring transcription re-initiation at each intergenic region.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L ...protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication. Transcription of the six genes occurs sequentially. This implies ending and re-initiating mRNA synthesis at each intergenic region (IGR). We explored here to which extent the binding of the X domain of P (XD) to the C-terminal region of the N protein (NTAIL) is involved in maintaining the P/L complex anchored to the nucleocapsid template during the sequential transcription. Amino acid substitutions introduced in the XD-binding site on NTAIL resulted in a wide range of binding affinities as determined by combining protein complementation assays in E. coli and human cells and isothermal titration calorimetry. Molecular dynamics simulations revealed that XD binding to NTAIL involves a complex network of hydrogen bonds, the disruption of which by two individual amino acid substitutions markedly reduced the binding affinity. Using a newly designed, highly sensitive dual-luciferase reporter minigenome assay, the efficiency of re-initiation through the five measles virus IGRs was found to correlate with NTAIL/XD KD. Correlatively, P transcript accumulation rate and F/N transcript ratios from recombinant viruses expressing N variants were also found to correlate with the NTAIL to XD binding strength. Altogether, our data support a key role for XD binding to NTAIL in maintaining proper anchor of the P/L complex thereby ensuring transcription re-initiation at each intergenic region.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We have recently developed a 2P2I HUNTER learning machine tool for filtering potential orthosteric PPI modulators. In the present research article we applied our algorithm to 8.3 million compounds ...representing the main chemical providers commercially available to design a PPI-focused library, 2P2I REF , composed of 143 218 small molecules. Compounds corresponding to medicinally important privileged structures identified as core structures in numerous therapeutics were prioritized in a medicinal oriented version of this database (2P2I PRIV – 51 476 compounds). A diverse chemical library was generated using 2D molecular fingerprints (2P2I DIV – 8217 diverse compounds). The carbon bond saturation index (Fsp3) was used as a final filter (Fsp3 ≥ 0.4) to escape from flatland, another hurdle in the long path to the gold mine. We analyzed the resulting chemical space of this final library of 1683 compounds, 2P2I 3D and discuss the chemical moieties proposed to the community. This library will now be tested to evaluate its ability to enhance hit rates in general screening campaigns and is open to academic and private companies for collaborative prospects.
Drugdrug interaction potential (DDI), especially cytochrome P450 (CYP) 3A4 inhibition potential, is one of the most important parameters to be optimized before preclinical and clinical ...pharmaceutical development as regard to the number of marketed drug metabolized mainly by this CYP and potentially co‐administered with the future drug. The present study aims to develop in silico models for CYP3A4 inhibition prediction to help medicinal chemists during the discovery phase and even before the synthesis of new chemical entities (NCEs), focusing on NCEs devoid of any inhibitory potential toward this CYP. In order to find a relevant relationship between CYP3A4 inhibition and chemical features of the screened compounds, we applied a genetic‐algorithm‐based QSAR exploratory tool SQS (Stochastic QSAR Sampler) in combination with different description approaches comprising alignment‐independent Volsurf descriptors, ISIDA fragments and Topological Fuzzy Pharmacophore Triplets. The experimental data used to build models were extracted from an in‐house database. We derived a model with good prediction ability that was confirmed on both newly synthesized compound and public dataset retrieved from Pubchem database. This model is a promising efficient tool for filtering out potentially problematic compounds.
N-Hydroxy-
N′-phenylthiourea and
N-hydroxy-
N′-phenylurea analogues were designed and evaluated as inhibitors of tyrosinase and melanin formation. The structure of the most active analogue
1 is ...reported.
A series of
N-hydroxy-
N′-phenylthiourea and
N-hydroxy-
N′-phenylurea analogues were prepared and evaluated as inhibitors of tyrosinase and melanin formation. The most active analogue
1 inhibited mushroom tyrosinase with an IC
50 of around 0.29
μM and also retained a substantial potency in cell culture by reducing pigment synthesis by 78%. Therefore, compound
1 could be considered as a promising candidate for preclinical drug development for skin hyperpigmentation application.
Dimeric cinnamoylamide derivatives were synthetized and tested as inhibitors of tyrosinase activity and melanin formation. The most active dimeric cinnamoylamide derivatives was dimeric compound of ...p-coumaric acid (compound 1) that inhibited tyrosinase activity more efficiently than p-coumaric acid. It also inhibited melanin production by B16 melanoma cell line and normal human melanocytes more efficiently than kojic acid. We next investigated the potential mutagenic and skin sensitization effect of compound 1. Compound 1 was found to induce no mutagenic activity, no irritation and no delayed contact hypersensitivity at the maximum concentration of 10%. In vitro percutaneous absorption studies exhibited that compound 1 could diffuse across the skin till its site of action. All these results lead us to propose that compound 1 may be a safe and effective candidate for treating skin hyperpigmentation related disorders.
Increased production and accumulation of melanin lead to hyperpigmentation disorders. Several inhibitors of tyrosinase, the key enzyme in melanin synthesis have been developed but exhibited lack of ...efficiency or some adverse side effects. Therefore, it appears very important to find new agents that will be able to promote inhibition of tyrosinase and pigmentation. In this study, some phenylalkylcinnamide molecules were synthesized and evaluated for their ability to act as tyrosinase inhibitors. Compounds 2 (IC50=0.03 mM) and 12 (IC50=0.028 mM) showed strong tyrosinase inhibitory potential comparable to standard hydroquinone (IC50=0.037 mM). Taken together, compounds 2 and 12 can be considered as good candidates for further investigations to evaluate their effect on the inhibition of melanin synthesis and skin pigmentation.
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