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John A Robinson

Publications and source records attributed to John A Robinson.

At least 19 recordsLinked to original sources
PubMed2007

Structure-guided peptidomimetic design leads to nanomolar beta-hairpin inhibitors of the Tat-TAR interaction of bovine immunodeficiency virus.

The Tat protein of immunodeficiency viruses is the main activator of viral gene expression. By binding specifically to its cognate site, the transactivator response element (TAR), Tat mediates a strong induction of the production of all viral transcripts. In seeking a new chemical solution to inhibiting viral protein-RNA interactions, we recently identified inhibitors of the viral Tat protein from the bovine immunodeficiency virus (BIV) using conformationally constrained beta-hairpin peptidomimetics. We identified a micromolar ligand, called BIV2, and the structure of its complex with BIV TAR was determined by NMR. In this work, we demonstrate that this chemistry can rapidly yield highly potent and selective ligands. On the basis of the structure, we synthesized and assayed libraries of mutant peptidomimetics. Remarkably, we were able in just a few rounds of design and synthesis to discover nanomolar inhibitors of the Tat-TAR interaction in BIV that selectively bind the BIV TAR RNA compared to RNA structures as closely related as the HIV-1 TAR or RRE elements. The molecular recognition principles developed in this study have been exploited in discovering related peptidomimetic inhibitors of the Tat-TAR interaction in HIV-1.

Amino Acid Sequence↗
PubMed2006

Discovery of novel, highly potent and selective beta-hairpin mimetic CXCR4 inhibitors with excellent anti-HIV activity and pharmacokinetic profiles.

Novel highly potent CXCR4 inhibitors with good pharmacokinetic properties were designed and optimized starting from the naturally occurring beta-hairpin peptide polyphemusin II. The design involved incorporating important residues from polyphemusin II into a macrocyclic template-bound beta-hairpin mimetic. Using a parallel synthesis approach, the potency and ADME properties of the mimetics were optimized in iterative cycles, resulting in the CXCR4 inhibitors POL2438 and POL3026. The inhibitory potencies of these compounds were confirmed in a series of HIV-1 invasion assays in vitro. POL3026 showed excellent plasma stability, high selectivity for CXCR4, favorable pharmacokinetic properties in the dog, and thus has the potential to become a therapeutic compound for application in the treatment of HIV infections (as an entry inhibitor), cancer (for angiogenesis suppression and inhibition of metastasis), inflammation, and in stem cell transplant therapy.

Animals↗
PubMed2006

Wnt/beta-catenin signaling is a normal physiological response to mechanical loading in bone.

A preliminary expression profiling analysis of osteoblasts derived from tibia explants of the high bone mass LRP5 G171V transgenic mice demonstrated increased expression of canonical Wnt pathway and Wnt/beta-catenin target genes compared with non-transgenic explant derived osteoblasts. Therefore, expression of Wnt/beta-catenin target genes were monitored after in vivo loading of the tibia of LRP5 G171V transgenic mice compared with non-transgenic mice. Loading resulted in the increased expression of Wnt pathway and Wnt/beta-catenin target genes including Wnt10B, SFRP1, cyclin D1, FzD2, WISP2, and connexin 43 in both genotypes; however, there was a further increased in transcriptional response with the LRP5 G171V transgenic mice. Similar increases in the expression of these genes (except cyclin D1) were observed when non-transgenic mice were pharmacologically treated with a canonical Wnt pathway activator, glycogen synthase kinase 3beta inhibitor and then subjected to load. These in vivo results were further corroborated by in vitro mechanical loading experiments in which MC3T3-E1 osteoblastic cells were subjected to 3400 microstrain alone for 5 h, which increased the expression of Wnt10B, SFRP1, cyclin D1, FzD2, WISP2, and connexin 43. Furthermore, when MC3T3-E1 cells were treated with either glycogen synthase kinase 3beta inhibitor or Wnt3A to activate Wnt signaling and then subjected to load, a synergistic up-regulation of these genes was observed compared with vehicle-treated cells. Collectively, the in vivo and in vitro mechanical loading results support that Wnt/beta-catenin signaling is a normal physiological response to load and that activation of the Wnt/beta-catenin pathway enhances the sensitivity of osteoblasts/osteocytes to mechanical loading.

Animals↗
PubMed2006

Identification of a PTH regulated gene selectively induced in vivo during PTH-mediated bone formation.

The biological activities of parathyroid hormone (PTH) on bone are quite complex as demonstrated by its catabolic and anabolic activities on the skeleton. Although there have been many reports describing genes that are regulated by PTH in osteoblast cells, the goal of this study was to utilize a well-established in vivo PTH anabolic treatment regimen to identify genes that mediate bone anabolic effects of PTH. We identified a gene we named PTH anabolic induced gene in bone (PAIGB) that has been reported as brain and acute leukemia cytoplasmic (BAALC). Therefore, using the latter nomenclature, we have discovered that BAALC is a PTH-regulated gene whose mRNA expression was selectively induced in rat tibiae nearly 100-fold (maximal) by a PTH 1-34 anabolic treatment regimen in a time-dependent manner. Although BAALC is broadly expressed, PTH did not regulate BAALC expression in other PTH receptor expressing tissues and we find that the regulation of BAALC protein by PTH in vivo is confined to mature osteoblasts. Further in vitro studies using rat UMR-106 osteoblastic cells show that PTH 1-34 rapidly induces BAALC mRNA expression maximally by 4 h while the protein was induced by 8 h. In addition to being regulated by PTH 1-34, BAALC expression can also be induced by other bone forming factors including PGE(2) and 1,25 dihydroxy vitamin D(3). We determined that BAALC is regulated by PTH predominantly through the cAMP/PKA pathway. Finally, we demonstrate in MC3T3-E1 osteoblastic cells that BAALC overexpression regulates markers of osteoblast differentiation, including downregulating alkaline phosphatase and osteocalcin expression while inducing osteopontin expression. We also demonstrate that these transcriptional responses mediated by BAALC are similar to the responses elicited by PTH 1-34. These data, showing BAALC overexpression can mimic the effect of PTH on markers of osteoblast differentiation, along with the observations that BAALC is induced selectively with a bone anabolic treatment regimen of PTH (not a catabolic treatment regimen), suggest that BAALC may be an important mediator of the PTH anabolic action on bone cell function.

Amino Acid Sequence↗
PubMed2006

Protein ligand design: from phage display to synthetic protein epitope mimetics in human antibody Fc-binding peptidomimetics.

Phage display is a powerful method for selecting peptides with novel binding functions. Synthetic peptidomimetic chemistry is a powerful tool for creating structural diversity in ligands as a means to establish structure-activity relationships. Here we illustrate a method of bridging these two methodologies, by starting with a disulfide bridged phage display peptide which binds a human antibody Fc fragment (Delano et al. Science 2000, 287, 1279) and creating a backbone cyclic beta-hairpin peptidomimetic with 80-fold higher affinity for the Fc domain. The peptidomimetic is shown to adopt a well-defined beta-hairpin conformation in aqueous solution, with a bulge in one beta-strand, as seen in the crystal structure of the phage peptide bound to the Fc domain. The higher binding affinity of the peptidomimetic presumably reflects the effect of constraining the free ligand into the conformation required for binding, thus highlighting in this example the influence that ligand flexibility has on the binding energy. Since phage display peptides against a wide variety of different proteins are now accessible, this approach to synthetic ligand design might be applied to many other medicinally and biotechnologically interesting target proteins.

Biomimetic Materials↗
PubMed2006

Structure-activity studies in a family of beta-hairpin protein epitope mimetic inhibitors of the p53-HDM2 protein-protein interaction.

Inhibitors of the interaction between the p53 tumor-suppressor protein and its natural human inhibitor HDM2 are attractive as potential anticancer agents. In earlier work we explored designing beta-hairpin peptidomimetics of the alpha-helical epitope on p53 that would bind tightly to the p53-binding site on HDM2. The beta-hairpin is used as a scaffold to display energetically hot residues in an optimal array for interaction with HDM2. The initial lead beta-hairpin mimetic, with a weak inhibitory activity (IC(50)=125 microM), was optimized to afford cyclo-(L-Pro-Phe-Glu-6ClTrp-Leu-Asp-Trp-Glu-Phe-D-Pro) (where 6ClTrp=L-6-chlorotryptophan), which has an affinity almost 1,000 times higher (IC(50)=140 nM). In this work, insights into the origins of this affinity maturation based on structure-activity studies and an X-ray crystal structure of the inhibitor/HDM2(residues 17-125) complex at 1.4 A resolution are described. The crystal structure confirms the beta-hairpin conformation of the bound ligand, and also reveals that a significant component of the affinity increase arises through new aromatic/aromatic stacking interactions between side chains around the hairpin and groups on the surface of HDM2.

Amino Acid Sequence↗
PubMed2006

Synthesis, solution structure and immune recognition of an epidermal growth factor-like domain from Plasmodium falciparum merozoite surface protein-1.

The Plasmodium falciparum merozoite surface protein-1 19 kDa fragment (MSP-1(19)) comprises two closely packed EGF-like domains (EGF=epidermal growth factor), each stabilized by three disulfide bonds. The native conformation of this protein is important for eliciting P. falciparum growth inhibitory antibodies. Here we show that the N-terminal EGF domain alone can be chemically synthesized and efficiently refolded to a native-like state, as shown by its solution structure as determined by NMR spectroscopy. In order to study its immunogenicity, the domain was coupled through its N terminus to a phospholipid and incorporated into reconstituted influenza virus-like particles (virosomes). When used to immunize mice, the peptide-loaded virosomes elicited potent humoral immune responses that were shown by Western blots and immunofluorescence assays to cross-react with native MSP-1 on the surfaces of P. falciparum blood stage parasites. This opens the way for a medicinal chemistry-oriented approach to the study and optimization of the antigenicity of the protein as a potential malaria vaccine candidate, whilst exploiting the immunopotentiating properties of influenza virosomes as a delivery vehicle.

Amino Acid Sequence↗
PubMed2006

Adaptive prediction trees for image compression.

This paper presents a complete general-purpose method for still-image compression called adaptive prediction trees. Efficient lossy and lossless compression of photographs, graphics, textual, and mixed images is achieved by ordering the data in a multicomponent binary pyramid, applying an empirically optimized nonlinear predictor, exploiting structural redundancies between color components, then coding with hex-trees and adaptive runlength/Huffman coders. Color palettization and order statistics prefiltering are applied adaptively as appropriate. Over a diverse image test set, the method outperforms standard lossless and lossy alternatives. The competing lossy alternatives use block transforms and wavelets in well-studied configurations. A major result of this paper is that predictive coding is a viable and sometimes preferable alternative to these methods.

Algorithms↗
PubMed2005

Crystal structure of an NPNA-repeat motif from the circumsporozoite protein of the malaria parasite Plasmodium falciparum.

A crystal structure is reported of the peptide Ac-Ala-Asn-Pro-Asn-Ala-NH2, representing the immunodominant region of the major surface protein on the malaria parasite; the NPNA motif adopts a type-I beta-turn, which is stabilized by hydrogen bonding between the CO of Asn2 and the NH of Ala5 as well as between the O(delta) of Asn2 and the NH of Asn4.

Amino Acid Motifs↗
PubMed2005

TAR RNA recognition by a cyclic peptidomimetic of Tat protein.

The search for new antiviral drugs that repress HIV viral replication by blocking transactivation of viral RNA transcription has long been advocated as an approach to novel antiviral therapy. However, research in this area has so far failed to yield attractive lead compounds because of the insufficient development of RNA-based medicinal chemistry. One difficulty in efforts to inhibit protein-RNA interactions using small druglike molecules is the large surface areas typically found at these interfaces. To overcome this problem, we sought to identify constrained peptidomimetic inhibitors that would provide potential new drug leads. We previously reported the discovery of a cyclic peptide mimic of the RNA-binding domain of BIV Tat protein based on a designed beta-hairpin scaffold. We demonstrated that the cyclic peptide bound BIV TAR RNA with an affinity comparable to that of the RNA-binding domain of the Tat protein and inhibited protein binding to the RNA. In this study, we report the structure of the complex of the cyclic peptide bound to BIV TAR RNA determined using heteronuclear NMR methods. The structure reveals a beta-hairpin conformation in the bound peptide, which adopts an unexpected orientation in the major groove of the RNA opposite those observed for peptides derived from the Tat protein. This structure suggests many ways in which to optimize the compound and enhance its activity and pharmacological potential and represents a further step in the rational design of a new class of HIV-1 virus replication inhibitors based on peptidomimetic chemistry.

Base Sequence↗
PubMed2005

Properties and structure-activity studies of cyclic beta-hairpin peptidomimetics based on the cationic antimicrobial peptide protegrin I.

The properties and structure-activity relationships (SAR) of a macrocyclic analogue of porcine protegrin I (PG-I) have been investigated. The lead compound, having the sequence cyclo-(-Leu-Arg-Leu-Lys-Lys-Arg-Arg-Trp-Lys-Tyr-Arg-Val-d-Pro-Pro-), shows antimicrobial activity against Gram-positive and -negative bacteria, but a much lower haemolytic activity and a much reduced ability to induce dye release from phosphatidylcholine/phosphatidylglycerol liposomes, when compared to PG-I. The enantiomeric form of the lead peptide shows comparable antimicrobial activity, a property shared with other cationic antimicrobial peptides acting on cell membranes. SAR studies involving the synthesis and biological profiling of over 100 single site substituted analogues, showed that the antimicrobial activity was tolerant to a large number of the substitutions tested. Some analogues showed slightly improved antimicrobial activities (2-4-fold lowering of MICs), whereas other substitutions caused large increases in haemolytic activity on human red blood cells.

Antimicrobial Cationic Peptides↗
PubMed2005

An improved solid-phase methodology for the synthesis of putative hexa- and heptapeptide intermediates in vancomycin biosynthesis.

The biosynthesis of the vancomycin aglycone involves three oxidative phenol coupling reactions, each catalyzed by a discrete cytochrome P450-like enzyme. Studies on the mechanism and specificity of the enzyme (called OxyB) catalyzing the first coupling, require access to suitable linear peptide precursors, each conjugated as a thioester to a peptide carrier domain of the vancomycin non-ribosomal peptide synthetase. An efficient route to representative free linear peptides is described here. The method makes use of Alloc-chemistry during solid-phase assembly of the peptide backbone, but importantly and in contrast to earlier efforts, largely avoids the use of amino acid side chain protecting groups. In this way, the target linear peptides can be released directly from the solid support under very mild conditions.

Nuclear Magnetic Resonance, Biomolecular↗
PubMed2005

Fragment memories mark the end of childhood amnesia.

Adults described and dated two kinds of first remembrances: a personal event memory (the recollection of a personal episode that had occurred at some time in some place) and a memory fragment (an isolated memory moment having no event context and remembered, perhaps, as an image, a behavior, or an emotion). First fragment memories were judged to have originated substantially earlier in life than first event memories--approximately 3 1/3 years of age for first fragment memories versus roughly 4 years of age for first event memories. We conclude that the end of childhood amnesia is marked not by our earliest episodic memories, but by the earliest remembered fragments of childhood experiences.

Adult↗
PubMed2004

Structural mimicry of retroviral tat proteins by constrained beta-hairpin peptidomimetics: ligands with high affinity and selectivity for viral TAR RNA regulatory elements.

An approach is described to the design of beta-hairpin peptidomimetic ligands for bovine immunodeficiency virus (BIV) Tat protein, which inhibit binding to its transactivator response element (TAR) RNA. A library of peptidomimetics was derived by grafting onto a hairpin-inducing d-Pro-l-Pro template sequences related to the RNA recognition element in Tat. One hairpin mimetic was identified that binds tightly (K(d) approximately 150 nM) to BIV TAR, and another that binds also to HIV-1 TAR RNA (K(d) approximately 1-2 microM). (In the same assay, the wild-type BIV Tat(65-81) peptide binds to BIV TAR with K(d) approximately 50 nM.) The high-affinity BIV-Tat mimetic was shown to adopt a stable beta-hairpin conformation in free solution by NMR methods. Amino acid substitutions in this mimetic were shown to impact on the hairpin structure and to disrupt binding to the RNA. This family of conformationally constrained peptidomimetics affords insights into the structural requirements for binding to TAR RNA and provides a basis for the design of new ligands with increased inhibitory activity and specificity to both BIV and HIV TAR RNAs.

Amino Acid Sequence↗
PubMed2003

Cell growth regulatory role of Runx2 during proliferative expansion of preosteoblasts.

The Runx2 (CBFA1/AML3/PEBP2alphaA) transcription factor promotes lineage commitment and differentiation by activating bone phenotypic genes in postproliferative osteoblasts. However, the presence of Runx2 in actively dividing osteoprogenitor cells suggests that the protein may also participate in control of osteoblast growth. Here, we show that Runx2 is stringently regulated with respect to cell cycle entry and exit in osteoblasts. We addressed directly the contribution of Runx2 to bone cell proliferation using calvarial osteoblasts from wild-type and Runx2-deficient mice (i.e., Runx2(-/-) and Runx2(DeltaC/DeltaC)). Runx2(DeltaC/DeltaC) mice express a protein lacking the Runx2 COOH terminus, which integrates several cell proliferation-related signaling pathways (e.g., Smad, Yes/Src, mitogen-activated protein kinase, and retinoblastoma protein). Calvarial cells but not embryonic fibroblasts from Runx2(-/-) or Runx2(DeltaC/DeltaC) mutant mice exhibit increased cell growth rates as reflected by elevations of DNA synthesis and G(1)-S phase markers (e.g., cyclin E). Reintroduction of Runx2 into Runx2(-/-) calvarial cells by adenoviral delivery restores stringent cell growth control. Thus, Runx2 regulates normal osteoblast proliferation, and the COOH-terminal region is required for this biological function. We propose that Runx2 promotes osteoblast maturation at a key developmental transition by supporting exit from the cell cycle and activating genes that facilitate bone cell phenotype development.

Animals↗