Survivin is one of the most tumor-specific genes in the human genome and is an attractive target for cancer therapy. However, small-molecule ligands for survivin have not yet been described. Thus, an interrogation of survivin which could potentially both validate a small-molecule therapy approach, and determine the biochemical nature of any of survivin’s functions has not been possible. Here we describe the discovery and characterization of a small molecule binding site on the survivin surface distinct from the Smac peptide-binding site. The new site is located at the dimer interface and exhibits many of the features of highly druggable, biologically relevant protein binding sites. A variety of small hydrophobic compounds were found that bind with moderate affinity to this binding site, from which one lead was developed into a group of compounds with nanomolar affinity. Additionally, a subset of these compounds are adequately water-soluble and cell-permeable. Thus, the structural studies and small molecules described here provide tools that can be used to probe the biochemical role(s) of survivin, and may ultimately serve as a basis for the development of small molecule therapeutics acting via direct or allosteric disruption of binding events related to this poorly understood target.

Methionine aminopeptidase-2 (MetAP2) is a novel target for cancer therapy. As part of an effort to discover orally active reversible inhibitors of MetAP2, a series of anthranilic acid sulfonamides with micromolar affinities for human MetAP2 were identified using affinity selection by mass spectrometry (ASMS) screening. These micromolar hits were rapidly improved to nanomolar leads on the basis of insights from protein crystallography; however, the compounds displayed extensive binding to human serum albumin and had limited activity in cellular assays. Modifications based on structural information on the binding of lead compounds to both MetAP2 and domain III of albumin allowed the identification of compounds with significant improvements in both parameters, which showed good cellular activity in both proliferation and methionine processing assays.

Antiapoptotic Bcl-2 family proteins inhibit apoptosis in cultured cells by binding BH3 domains of proapoptotic Bcl-2 family members via a hydrophobic BH3 binding groove on the protein surface. We investigated the physiological importance of the BH3 binding groove of an antiapoptotic Bcl-2 protein in mammals in vivo by analyzing a viral Bcl-2 family protein. We show that the gamma-herpesvirus 68 (gammaHV68) Bcl-2 family protein (gammaHV68 v-Bcl-2), which is known to inhibit apoptosis in cultured cells, inhibits both apoptosis in primary lymphocytes and Bax toxicity in yeast. Nuclear magnetic resonance determination of the gammaHV68 v-Bcl-2 structure revealed a BH3 binding groove that binds BH3 domain peptides from proapoptotic Bcl-2 family members Bax and Bak via a molecular mechanism shared with host Bcl-2 family proteins, involving a conserved arginine in the BH3 peptide binding groove. Mutations of this conserved arginine and two adjacent amino acids to alanine (SGR to AAA) within the BH3 binding groove resulted in a properly folded protein that lacked the capacity of the wild-type gammaHV68 v-Bcl-2 to bind Bax BH3 peptide and to block Bax toxicity in yeast. We tested the physiological importance of this v-Bcl-2 domain during viral infection by engineering viral mutants encoding a v-Bcl-2 containing the SGR to AAA mutation. This mutation resulted in a virus defective for both efficient reactivation of gammaHV68 from latency and efficient persistent gammaHV68 replication. These studies demonstrate an essential functional role for amino acids in the BH3 peptide binding groove of a viral Bcl-2 family member during chronic infection.

Novel antitumour drug Bcl-2 proteins are important regulators of programmed cell death (apoptosis) and are overexpressed in many cancers, contributing to tumour growth and resistance to treatment. Some of the latest techniques in drug design, including NMR-based screening, parallel synthesis, and structure-based design, have been used to develop a new small-molecule Bcl-2 inhibitor called ABT-737. It is three orders of magnitude more potent than any previous Bcl-2 inhibitor, and it looks as if this compound could be useful therapeutically. On its own, ABT-737 kills some cancer cell lines, including cells from lymphoma and small-cell lung carcinomas; in addition, it enhances the effects of chemotherapeutics and radiation on other cancer cell lines.

2531 Methionine aminopeptidase-2 (MetAP2), an intracellular enzyme responsible for the removal of the N-terminal initiator methionine from nascent proteins, has been suggested as a novel target for cancer therapy. As part of an effort to discover orally active reversible inhibitors of MetAP2, a series of anthranilic acid sulfonamides with micromolar affinities for human MetAP2 was identified by ASMS screening. These micromolar hits, typified by A-193400 (MetAP2 IC 50 = 13 μM) and A-444148 (MetAP2 IC 50 = 1.3 μM) were rapidly improved to nanomolar leads based on insights from protein crystallography. Compounds with good enzyme inhibitory activity and promising oral bioavailability in mice such as A-751277 (MetAP2 IC 50 = 0.010 μM, F = 93%) were obtained; however the compounds displayed extensive binding to HSA and had limited activity in cellular assays (EC 50 = 0.40 μM for HMVEC proliferation, EC 50 = 2.1 μM for HT-1080 proliferation). Modifications based on structural information on the binding of lead compounds to domain 3 of albumin allowed the identification of compounds with significant improvements in both parameters such as A-832234 (MetAP2 IC 50 = 0.011 μM, HMVEC EC 50 = 0.007 μM, HT-1080 EC 50 = 0.006 μM) and A-847519 (MetAP2 IC 50 = 0.017 μM, HT-1080 EC 50 = 0.036 μM) which show good cellular activity in both proliferation and methionine processing assays.

NMR studies of the antiapoptotic protein survivin have been used to determine the homodimer interface of the protein in solution and to identify residues of the protein that interact with Smac/Diablo. In solution, survivin(1-120) forms a bow-tie-shaped dimer whose interface is composed of its N-terminal residues as well as residues connecting its BIR domain to the C-terminal alpha helix. The solution structure resolves the controversy regarding the two possible dimer interfaces for survivin observed in X-ray crystal structures. The structural basis for the interaction between survivin and Smac/Diablo was also investigated. When Smac/Diablo or N-terminal Smac/Diablo peptide analogues are added to a solution of survivin, specific residues near alpha4 and beta3 are perturbed. NMR experiments indicate that the peptides bind across the third beta-strand of survivin in a manner similar to the way Smac/Diablo peptides bind to the BIR3 domain of X-linked IAP (XIAP).

The structures of two isoforms of Bcl-2 that differ by two amino acids have been determined by NMR spectroscopy. Because wild-type Bcl-2 behaved poorly in solution, the structures were determined by using Bcl-2/Bcl-x L chimeras in which part of the putative unstructured loop of Bcl-2 was replaced with a shortened loop from Bcl-x L . These chimeric proteins have a low pI compared with the wild-type protein and are soluble. The structures of the two Bcl-2 isoforms consist of 6 α-helices with a hydrophobic groove on the surface similar to that observed for the homologous protein, Bcl-x L . Comparison of the Bcl-2 structures to that of Bcl-x L shows that although the overall fold is the same, there are differences in the structural topology and electrostatic potential of the binding groove. Although the structures of the two isoforms of Bcl-2 are virtually identical, differences were observed in the ability of the proteins to bind to a 25-residue peptide from the proapoptotic Bad protein and a 16-residue peptide from the proapoptotic Bak protein. These results suggest that there are subtle differences in the hydrophobic binding groove in Bcl-2 that may translate into differences in antiapoptotic activity for the two isoforms.

The three‐dimensional structure of the anti‐apoptotic protein Bcl‐X L complexed to a 25‐residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl‐X L bound to a 16‐residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl‐X L . However, based upon site‐directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25‐mer for Bcl‐X L compared to the Bad 16‐mer. Rather, the increased helix propensity of the Bad 25‐mer is primarily responsible for its greater affinity for Bcl‐X L . Based on this observation, a pair of 16‐residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl‐X L . Both peptides showed an increase in helix propensity compared to the wild‐type and exhibited an enhanced affinity for Bcl‐X L .

C24-Deoxyascomycin was prepared in a two-step process from ascomycin and evaluated for its immunosuppressant activity relative to ascomycin and FK506. An intermediate in the synthetic pathway, Delta(23,24)-dehydroascomycin, was likewise evaluated. Despite lacking the hydrogen-bonding interactions associated with the C24-hydroxyl moiety of ascomycin, C24-deoxyascomycin was found to be equipotent to the parent compound both in its immunosuppressive potency and in its interaction with the immunophilin, FKBP12. Conversely, Delta(23,24)-dehydroascomycin which also lacks the same hydrogen-bonding interactions did not exhibit this potency. NMR studies were conducted on the FKBP12/C24-deoxyascomycin complex in an attempt to understand this phenomenon at the molecular level. The NMR structures of the complexes formed between FKBP12 and ascomcyin or C24-deoxyascomcyin were very similar, suggesting that hydrogen-bonding interactions with the C24 hydroxyl moiety are not important; for complex formation.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTImproved NMR Structures of Protein/Ligand Complexes Using Residual Dipolar CouplingsEdward T. Olejniczak, Robert P. Meadows, Hong Wang, Mengli Cai, David G. Nettesheim, and Stephen W. FesikView Author Information Pharmaceutical Discovery Division Abbott Laboratories, Abbott Park, Illinois 60064 Cite this: J. Am. Chem. Soc. 1999, 121, 39, 9249–9250Publication Date (Web):September 15, 1999Publication History Received23 June 1999Revised5 August 1999Published online15 September 1999Published inissue 1 October 1999https://doi.org/10.1021/ja992139jCopyright © 1999 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views131Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit Read OnlinePDF (161 KB) Get e-AlertsSUBJECTS:Conformation,Coupling reactions,Crystal structure,Ligands,Protein structure Get e-Alerts

Heterodimerization between members of the Bcl-2 family of proteins is a key event in the regulation of programmed cell death. The molecular basis for heterodimer formation was investigated by determination of the solution structure of a complex between the survival protein Bcl-x L and the death-promoting region of the Bcl-2-related protein Bak. The structure and binding affinities of mutant Bak peptides indicate that the Bak peptide adopts an amphipathic α helix that interacts with Bcl-x L through hydrophobic and electrostatic interactions. Mutations in full-length Bak that disrupt either type of interaction inhibit the ability of Bak to heterodimerize with Bcl-x L .

THE Bcl-2 family of proteins regulate programmed cell death by an unknown mechanism1. Here we describe the crystal and solution structures of a Bcl-2 family member, Bcl-xL (ref. 2). The structures consist of two central, primarily hydrophobic α-helices, which are surrounded by amphipathic helices. A 60-residue loop connecting helices αl and α2 was found to be flexible and non-essential for anti-apoptotic activity. The three functionally important Bcl-2 homology regions (BH1, BH2 and BH3)3–5 are in close spatial proximity and form an elongated hydrophobic cleft that may represent the binding site for other Bcl-2 family members. The arrangement of the α-helices in Bcl-xL is reminiscent of the membrane translocation domain of bacterial toxins, in particular diphtheria toxin and the colicins6. The structural similarity may provide a clue to the mechanism of action of the Bcl-2 family of proteins.

The amino-terminal fragment (ATF) of urokinase-type plasminogen activator is a two domain protein which consists of a growth factor and a kringle domain. The H-1, C-13, and N-15 chemical shifts of this protein have been assigned using heteronuclear two- and three-dimensional NMR experiments on selective and uniformly N-15- and N-15/C-13-labeled protein isolated from mammalian cells that overexpress the protein. The chemical shift assignments were used to interpret the NOE data which resulted in a total of 1299 NOE restraints. The NOE restraints were used along with 27 phi angle restraints and 21 hydrogen-bonding restraints to produce 15 low energy structures. The individual domains in the structures are highly converged, but the two domains are structurally independent. The root mean square deviations (rmsd) between residues 11-46 in the growth factor domain and the mean atomic coordinates were 0.99 +/- 0.2 for backbone heavy atoms and 1.65 +/- 0.2 for all non-hydrogen atoms. For residues 55-130 in the kringle domain, the rmsd was 0.84 +/- 0.2 for backbone heavy atoms and 1.42 +/- 0.2 for all non-hydrogen atoms. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor and other homologous proteins were observed in the region which has been implicated in binding the urokinase receptor which may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor.

The oxidation of Co(II) bleomycin A2 by dioxygen leads to two products, HO2-Co(III) bleomycin A2 (form I) and Co(III) bleomycin A2 (form II). 1H NMR chemical shift assignments for protons of both forms have been made by two-dimensional NMR spectral techniques. The chemical shifts of protons throughout forms I and II differ from each other and from apobleomycin A2. NOESY spectra reveal a number of intermediate and long-range 1H-1H couplings within the metal-binding domain, between the metal-binding domain and the peptide linker, which connects it and the DNA-binding region of the molecule, and, in form I, between the DNA- and metal-binding domains. Molecular dynamics calculations were carried out based on the NOESY results and an adjustable square pyramidyl ligand geometry around Co(III) composed of nitrogen atoms of the primary and secondary amine groups, pyridine (N5), and amide and imidazole (N1) of the hydroxyhistidine residue. In form I, the bithiazole group folds back across the square pyramid forming a compact structure. Although this conformational feature was not observed in form II, the peptide linker between the metal- and DNA-binding domains in both species shows extensive folding based on a large number of intramolecular interactions.

The 1H, 13C, and 15N resonances of FKBP when bound to the immunosuppressant, ascomycin, were assigned using a computer-aided analysis of heteronuclear double and triple resonance three-dimensional nmr spectra of [U-15N]FKBP/ascomycin and [U-15N,13C]FKBP/ascomycin. In addition, from a preliminary analysis of two heteronuclear four-dimensional data sets, 3JHN,H alpha coupling constants, amide exchange data, and the differences between the C alpha and C beta chemical shifts of FKBP to random coil values, the secondary structure of FKBP when bound to ascomycin was determined. The secondary structure of FKBP when bound to ascomycin in solution closely resembled the x-ray structure of the FKBP/FK506 complex but differed in some aspects from the structure of uncomplexed FKBP in solution.