Temperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein.

Escherichia coli strain LE316 contains a mutation in gyrB that results in the substitution of Val164 to Gly and confers both chlorobiocin resistance and temperature sensitivity. Selection for suppressors of the ts phenotype yielded second-site mutations in GyrB at His38 and Thr157. The properties of proteins bearing these mutations have been characterized, and a mechanism of suppression is proposed based upon structural considerations.

Hydroxylated 2-(5'-salicyl)naphthalenes as protein-tyrosine kinase inhibitors.

The salicyl group figures prominently in several potent protein-tyrosine kinase (PTK) inhibitors, including the fermentation product lavendustin A (3), the salicylsulfonyl nitrostyryl 30, and our recently reported salicyl-containing stilbene 7. Taking compound 7 and the isomeric 8 as lead structures, bicyclic nuclei 9-12 were prepared as conformationally constrained mimetics in which the hydroxyphenyl rings of 7 and 8 are held coplanar with the stilbene ethylene bridge. A similar approach with styryl-based PTK inhibitors of structure 1 previously yielded analogues 2 with enhanced potency. In the present case, however, the resulting salicyl-containing bicyclics exhibited extremely poor inhibitory potency when examined against autophosphorylation of immunoprecipitated p56lck PTK preparations. The implications of these results are discussed as they relate to the potential ways in which salicyl-containing stilbenes may be oriented relative to styryl-based inhibitors of type 1 and to an emerging class of potent aryl-substituted bicyclic inhibitors exemplified by compound 31.

Non-amine based analogues of lavendustin A as protein-tyrosine kinase inhibitors.

The fermentation product lavendustin A (1) is a protein-tyrosine kinase (PTK) inhibitor whose active pharmacophore has previously been shown to reside in the more simplified salicyl-containing benzylamine 2. Amine 2 bears some structural resemblance to two other natural product PTK inhibitors, erbstatin (3) and piceatannol (4). Non-amine containing analogues of 2 were therefore synthesized which incorporated additional aspects of either erbstatin or piceatannol. Examination of these inhibitors in immunoprecipitated p56lck, epidermal growth factor receptor (EGFR), and c-erb B-2/HER 2/neu PTK preparations showed that compound 12 (IC50 = 60 nM) was one of the most potent p56lck inhibitors reported to date. These results demonstrate that nitrogen is not an essential component of the lavendustin A pharmacophore 2 and that 1,2-diarylethanes and -ethenes bearing a salicyl moiety appear to be valuable structural motifs for the construction of extremely potent PTK inhibitors.

Fibrinogen receptor (GPIIb-IIIa) antagonists derived from 5,6-bicyclic templates. Amidinoindoles, amidinoindazoles, and amidinobenzofurans containing the N-alpha-sulfonamide carboxylic acid function as potent platelet aggregation inhibitors.

A series of highly potent and specific fibrinogen receptor antagonists have been discovered and optimized through structural modification of the novel amidinoindole and benzofuran compounds, I and II. Systematic linker optimization afforded the amidinobenzofuran-containing inhibitor 29, which displayed an IC50 value of 250 nM in platelet aggregation assays. Attempts to enhance activity by modification of the beta-position of the beta-alanyl carboxylate group of 29 had only a modest effect on inhibitory activity in aggregation assays. Analogues prepared to enhance the activity by conformational restriction were also found to be equally or less potent. In contrast, modification at the alpha-position of the beta-alanyl carboxylate group resulted in the identification of extremely potent and novel amidinobenzofuran-containing derivatives 46-49. Reexamination of 5,6-bicyclic aromatic nucleus led to the further identification of amidinoindole- and amidinoindazole-containing derivatives 53-55. These analogues, 46-49 and 53-55, exhibited potent in vitro activity with IC50 values of 25-65 nM in platelet aggregation assays and an IC50 value of 2 nM in fibrinogen binding assays and demonstrated a selectivity of > 50,000-fold for GPIIb-IIIa versus the most closely related integrin, the vitronectin receptor, alpha v beta 3.

Use of conformationally restricted benzamidines as arginine surrogates in the design of platelet GPIIb-IIIa receptor antagonists.

The use of 5,6-bicyclic amidines as arginine surrogates in the design of a novel class of potent platelet glycoprotein IIb-IIIa receptor (GPIIb-IIIa) antagonists is described. The additional conformational restriction offered by the bicyclic nucleus results in 20-400-fold increases in potency compared to the freely flexible, acyclic benzamidine counterpart. The design, synthesis, structure-activity relationships (SAR), and in vitro activity of this novel class of GPIIb-IIIa antagonists are presented.

x ray crystallography.

x Ray crystallography is currently the most favoured technique for structure determination of proteins and biological macromolecules. Increasingly, those interested in all branches of the biological sciences require structural information to shed light on previously unanswered questions. Furthermore, the availability of a protein structure can provide a more detailed focus for future research. The extension of the technique to systems such as viruses, immune complexes, and protein-nucleic acid complexes serves only to widen the appeal of crystallography. Structure based drug design, site directed mutagenesis, elucidation of enzyme mechanisms, and specificity of protein-ligand interactions are just a few of the areas in which x ray crystallography has provided clarification.

Structural, biochemical and electrostatic basis of serotype specificity in bovine enteroviruses.

We have performed immunostructural analyses of three closely related picornaviruses in order to gain understanding of the biochemical and structural basis of serotype specificity. We carried out sequence alignments of the capsid regions of three bovine enterovirus strains: VG-5-27 and M-4 from serotype 1 and PS-87 from serotype 2. Using our knowledge of the three dimensional and antigenic structure of strain VG-5-27 and the high levels of sequence identity between the strains, we have calculated the structures and solvent-accessible electrostatic potentials of the epitopes of all three viruses. We have demonstrated the viability of the molecular models of the epitopes of the M-4 and PS-87 strains. In each of the strains, we have explained the serotype specificities in terms of specific physical and chemical properties, and identified individual residues which are pivotal in determination of antibody recognition. These changes are in agreement with the known cross-reactivity of peptide and antiviral sera, showing that it is possible to derive structures for short variable sections of proteins of high sequence identity using molecular modelling which are significant in terms of biological function. We believe this study to be a novel approach in the analysis of virus serotype specificity.

Picornavirus uncoating.

Recently, much has been learned about the molecular mechanisms involved in the pathogenesis of picornaviruses. This has been accelerated by the solving of the crystal structures of many members of this virus family. However, one stage of the virus life cycle remains poorly understood: uncoating. How do these simple but efficient pathogens protect their RNA genomes with a stable protein shell and yet manage to uncoat this genome at precisely the right time during infection? The purpose of this article is to review the current state of knowledge and the most recent theories that attempt to answer this question. The review is based extensively on structural data but also makes reference to the wealth of biochemical information on the topic.

Automated reticulocyte counting: evaluation of the Coulter STKS Haematology Analyser reticulocyte counting function.

This study evaluated reticulocyte counting with the automated reticulocyte function of the Coulter STKS Haematology Analyser. This is an upgrade option for Coulter STKS and MAXIM haematology analysers. Reticulocyte counts obtained with the automated reticulocyte counting function were compared with those obtained by visual counting. Reticulocyte counting with both methods gave excellent comparability with a correlation coefficient of 0.98. Results were consistent with the well documented imprecision of the manual method with a coefficient of variation (CV) of 16-22%. In contrast, the automated reticulocyte counting function was more precise with a CV of 12.3%. In both cases, counts were stable after storage for 24 h at room temperature and 4 degrees C. Our results suggest that the use of this upgrade will be beneficial for many laboratories.

Phosphonate inhibitors of protein-tyrosine and serine/threonine phosphatases.

In all, 15 aryl-containing phosphonates have been synthesized and tested for their effect on protein-tyrosine phosphatase (PTPase) activity. Two compounds, (naphth-2-yl) difluoromethylphosphonic acid (12) and (napthy-1-yl) difluoromethylphosphonic acid (13) have been found to inhibit dephosphorylation of [32P]insulin receptors by PTP-1B, a protein tyrosine phosphatase (PTPase), with IC50 values of 40-50 microM. Compound 12 competitively inhibited insulin-receptor dephosphorylation by PTP-1B. Compound 12 also inhibited PTP-1B-catalysed dephosphorylation of a synthetic tyrosine phosphorylated substrate poly(Glu80-Tyr20) at the same potency, indicating that 12 acted via interaction with the PTPase. Additionally, 12 inhibited insulin-receptor PTPase(s) and epridermal-growth-factor-receptor PTPase(s) present in solubilized membranes from CHO (Chinese-hamster ovary)/HIRc and A431 cells respectively. IC50 values of 40-50 microM were obtained in all cases with compound 12. Of note is the fact that these compounds did not have any effect on insulin-receptor autophosphorylation. Nine out of the 15 compounds potently inhibited serine/threonine phosphatase PP-2A activity without any effect on serine/threonine phosphatase PP-1 when tested at a concentration as high as 675 microM. The most potent compounds acting toward PP-2A had IC50 values of 45-50 microM. These PP-2A inhibitors could be useful tools for studying serine/threonine-phosphatase-mediated signal transduction. Two compounds, 12 and 13, inhibited both tyrosine phosphatase PTP-1B and serine/threonine phosphatase PP-2A with similar potency; IC50 values being 40-50 microM in both cases. Details of the synthesis of compounds 10, 11 and 13 are given in Supplementary Publication SUP 50177 (6 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1995) 305, 9.

Characterization of neutralizing antibodies to bovine enterovirus elicited by synthetic peptides.

Six synthetic peptides corresponding to regions of bovine enterovirus (BEV), strain VG-5-27, elicited antibodies in mice which reacted with the virus in various assays. These antibodies have been characterised on the basis of their ability to (1) neutralize the virus, (2) bind to the intact virus particle in an immunoprecipitation test, (3) react with the denatured viral proteins, and (4) give immunofluorescent staining of virus infected cells. We have also determined the proportion of antipeptide antibody which binds to the virus in each case. All of the sera immunoprecipitated the virus and neutralized its activity to varying extents. Two of the sera specific for VP 1 sequences failed to react with denatured VP 1 whereas all the other antisera reacted with their respective parental proteins. All of the sera reacted with VG-5-27 infected cells in an immunofluorescence test. The proportion of antibodies to each peptide recognizing intact virus was variable and did not appear to correlate with neutralizing activity. In addition, the ability of each of the sera to react with and neutralize three other strains of the virus was analysed. With one of these strains significant cross-neutralization was observed.

Conformational changes during proteolytic processing of a picornavirus capsid proteins.

We have used synthetic peptide antibodies to probe conformational changes that occur during the cleavage cascade which generates the capsid proteins of a picornavirus. The initial translation product of 97 kDa, the precursor of all four structural proteins, is cleaved to form a 63 kDa fragment which, we show, has significantly different folding characteristics to both its larger parent and its products. We demonstrate that proteolytic cleavages as distant as 520 residues from epitopes confer sufficiently large conformational changes as to render them unrecognisable. To our knowledge, this is the first demonstration of this phenomenon in the picornavirus system.

Chemically synthesized peptides elicit neutralizing antibody to bovine enterovirus.

Synthetic peptides representing 14 regions of the bovine enterovirus structural proteins were used to raise antibodies in mice. The peptides were predicted using amino acid sequence alignments with the position of antigenic sites on other picornaviruses. Five of the anti-peptide antibodies reacted with the virus in an immunoprecipitation test. Furthermore, each of these anti-peptide antibodies neutralized virus infectivity; those directed against peptides of VP2 and VP3 neutralized to a greater extent than those directed against peptides of VP1. The positions of these epitopes in the viral structural proteins are discussed in relation to corresponding positions in other picornaviruses.

Cyclic peptide inhibitors of phosphatidylinositol 3-kinase p85 SH2 domain binding.

Cyclic hexameric peptides based on the amino acid sequence "Gly-Xxx-Val-Pro-Met-Leu", where Xxx is either phosphotyrosyl (pTyr) residue or a hydrolytically stable pTyr mimetic, were examined for their ability to bind to the C-terminal SH2 domain of the p85 phosphoinositol 3-kinase (PI 3-kinase). The cyclic peptides retained significant binding affinity relative to their linear counterparts. Potency varied depending on Xxx in the order: phosphonomethyl phenylalanine (Pmp, ID50 = 5.2 microM) < phosphonodifluoromethyl phenylalanine (F2Pmp, ID50 = 2.2 microM) < pTyr (ID50 = 1.0 microM), with Xxx = Tyr being inactive (ID50 > 500 M). Greatly reduced potency was observed when Xxx was of the unnatural D-configuration. The cyclic peptides represent conformationally constrained ligands which should be useful in the development of p85 SH2 domain-directed inhibitors.

Nonhydrolyzable phosphotyrosyl mimetics for the preparation of phosphatase-resistant SH2 domain inhibitors.

Src homology 2 (SH2) domains participate in protein tyrosine kinase (PTK)-mediated cellular signal transduction through their ability to bind with high affinity to phosphotyrosyl (pTyr)-bearing protein sequences. Although peptides containing pTyr competitively inhibit the binding between phosphoproteins and cognate SH2 proteins in a sequence-specific manner, such peptides are rapidly dephosphorylated by cellular phosphatases. We now describe our efforts to develop SH2 inhibitory peptides containing phosphatase-resistant pTyr surrogates. The parent compound, (phosphonomethyl)phenylalanine (Pmp), is a phosphonate-based mimetic of pTyr in which the phosphate ester oxygen (> COPO3H2) has been replaced by a methylene unit (> CCX2PO3H2, X2 = H2). Pmp analogues bearing fluorine (X2 = H, F or X2 = F2) or hydroxyl (X2 = H, OH) substituents on the phosphonate alpha-methylene carbon have been prepared and incorporated into peptides for use as SH2 domain inhibitors. In an assay using the C-terminal SH2 domain of phosphatidylinositol (PI) 3-kinase, peptides having a GXVPML sequence [where X = pTyr, Pmp, hydroxy-Pmp (HPmp), monofluoro-Pmp (FPmp), and difluoro-Pmp (F2Pmp)] exhibited binding potency in the order HPmp < Pmp < FPmp < F2Pmp = pTyr. Distinct peptide sequences which bind selectively with Src and Grb2 SH2 domains were also prepared with pTyr and F2Pmp. The F2Pmp peptides bound with high (0.2- to 5-fold) relative affinity, compared to analogous pTyr peptides. We conclude that peptides containing F2Pmp bind to SH2 domains with high affinity and specificity and, being resistant to cellular phosphatases, should provide a generally useful tool for disrupting SH2 domain-mediated signaling pathways in intact cells.

Why is phosphonodifluoromethyl phenylalanine a more potent inhibitory moiety than phosphonomethyl phenylalanine toward protein-tyrosine phosphatases?

The phosphonodifluoromethyl phenylalanine (F2Pmp) is superior to phosphonomethyl phenylalanine (Pmp) as a non-hydrolyzable phosphotyrosine (pTyr) mimetic. The difluoromethyl moiety increases the inhibitory potency of a F2Pmp-containing peptide over a Pmp-containing counterpart by 1000-fold toward the protein tyrosine phosphatase (PTPase), PTP1. Fluorine substitution at the methylene carbon have the double effect of lowering the phosphonate pKa2 as well as introducing hydrogen bonding interactions similar to the phosphate ester oxygen in pTyr. The inhibition of PTP1-catalyzed dephosphorylation reaction by both the F2Pmp and Pmp-containing peptides did not vary as a function of pH. The data indicate that both the monoanion and the dianion forms of the phosphonate bind PTP1 with equal efficiency. Thus, the better binding by the F2Pmp-peptide as compared to the Pmp-peptide is not due to the difference in pKa2. Taken together, these results offer an explanation for the increased affinity of F2Pmp for PTP1. The two fluorine atoms in F2Pmp may be able to interact with active site residues in PTP1 in a fashion analogous to that involving the phenolic oxygen and side chains in the active site of PTP1. Ki measurements for a simple phosphonic acid, Pmp- and F2Pmp-containing peptides suggest that although the principal recognition element is F2Pmp itself, the surrounding amino acids are required for high affinity binding. Comparative analysis of the inhibition of PTP1, PTP alpha and LAR by F2Pmp-containing peptides suggests that selective, tight-binding PTPase inhibitors can be developed.

Spirocyclic nonpeptide glycoprotein IIb-IIIa antagonists. Part 1: design of potent and specific 3,9-diazaspiro[5.5]undecanes.

The synthesis and biological activity of novel glycoprotein IIb-IIla antagonists containing the 3,9-diazaspiro[5.5]undecane nucleus are described. The potent activity of these compounds as platelet aggregation inhibitors demonstrates the utility of the spirocyclic structures as a central template for nonpeptide RGD mimics.

Spirocyclic nonpeptide glycoprotein IIb-IIIa antagonists. Part 2: design of potent antagonists containing the 3-azaspiro[5.5]undecanes.

The synthesis and biological activity of novel glycoprotein IIb-IlIa anatagonists containing 3-azaspiro[5.5]undec-9-yl nucleus are described. The potent activity of these compounds as platelet aggregation inhibitors demonstrates the utility of the monoazaspirocyclic structure as central template for nonpeptide RGD mimics.