Exploiting polarity and chirality to probe the Hsp90 C-terminus

Inhibition of the Hsp90 C-terminus is an attractive therapeutic approach for the treatment of cancer. Novobiocin, the first Hsp90 C-terminal inhibitor identified, contains a synthetically complex noviose sugar that has limited the generation of structure-activity relationships for this region of the molecule. The work described herein utilizes various ring systems as noviose surrogates to explore the size and nature of the surrounding binding pocket.

Novobiocin Enhances Polymyxin Activity by Stimulating Lipopolysaccharide Transport

Gram-negative bacteria are challenging to kill with antibiotics due to their impenetrable outer membrane containing lipopolysaccharide (LPS). The polymyxins, including colistin, are the drugs of last resort for treating Gram-negative infections. These drugs bind LPS and disrupt the outer membrane; however, their toxicity limits their usefulness. Polymyxin has been shown to synergize with many antibiotics including novobiocin, which inhibits DNA gyrase, by facilitating transport of these antibiotics across the outer membrane. Recently, we have shown that novobiocin not only inhibits DNA gyrase but also binds and stimulates LptB, the ATPase that powers LPS transport. Here, we report the synthesis of novobiocin derivatives that separate these two activities. One analog retains LptB-stimulatory activity but is unable to inhibit DNA gyrase. This analog, which is not toxic on its own, nevertheless enhances the lethality of polymyxin by binding LptB and stimulating LPS transport. Therefore, LPS transport agonism contributes substantially to novobiocin-polymyxin synergy. We also report other novobiocin analogs that inhibit DNA gyrase better than or equal to novobiocin, but bind better to LptB and therefore have even greater LptB stimulatory activity. These compounds are more potent than novobiocin when used in combination with polymyxin. Novobiocin analogs optimized for both gyrase inhibition and LPS transport agonism may allow the use of lower doses of polymyxin, increasing its efficacy and safety.

From Intermolecular Interactions to Texture in Polycrystalline Surfaces of 1,ω-alkanediols (ω = 10-13)

Differences on herringbone molecular arrangement in two forms of long-chain 1,ω-alkanediols (C_nH_2n+2O₂ with n = 10, 11, 12, 13) are explained from the analysis of O-H···O hydrogen-bond sequences in infinite chains and the role of a C-H···O intramolecular hydrogen-bond in stabilization of a gauche defect, as well as the inter-grooving effectiveness on molecular packing. GIXD (Glancing Incidence X-ray Diffraction) experiments were conducted on polycrystalline monophasic samples. Diffracted intensities were treated with the multi-axial March-Dollase method to correlate energetic and geometrical features of molecular interactions with the crystalline morphology and textural pattern of samples. The monoclinic (P2₁/c, Z = 2) crystals of the even-numbered members (n = 10, 12; DEDOL and DODOL, respectively) are diametrical prisms with combined form {104}/{-104}/{001} and present a two-fold platelet-like preferred orientation, whereas orthorhombic (P2₁2₁2₁, Z = 4) odd-numbered members (n = 11, 13; UNDOL and TRDOL, respectively) present a dominant needle-like orientation on direction [101] (fiber texture). We show that crystalline structures of medium complexity and their microstructures can be determined from rapid GIXD experiments from standard radiation, combined with molecular replacement procedure using crystal structures of compounds with higher chain lengths as reference data.

Synthesis and biological evaluation of coumarin replacements of novobiocin as Hsp90 inhibitors

Since Hsp90 modulates all six hallmarks of cancer simultaneously, it has become an attractive target for the development of cancer chemotherapeutics. In an effort to develop more efficacious compounds for Hsp90 inhibition, novobiocin analogues were prepared by replacing the central coumarin core with naphthalene, quinolinone, and quinoline surrogates. These modifications allowed for modification of the 2-position, which was previously unexplored. Biological evaluation of these compounds suggests a hydrophobic pocket about the 2-position of novobiocin. Anti-proliferative activities of these analogues against multiple cancer cell lines identified 2-alkoxyquinoline derivatives to exhibit improved activity.

Novobiocin analogues with second-generation noviose surrogates

Hsp90 is a promising therapeutic target for the treatment of cancer. Novobiocin is the first Hsp90 C-terminal inhibitor ever identified and recent structure-activity relationship studies on the noviose sugar identified several commercially available amines as suitable surrogates. In an effort to further understand this region of the molecule, analogues containing various N'-amino substituents were prepared and evaluated against two breast cancer cell lines for determination of their efficacy. Compound 37j manifested the most potent anti-proliferative activity from these studies and induced Hsp90-dependent client protein degradation at mid nano-molar concentrations.

Synthesis and biological evaluation of arylated novobiocin analogs as Hsp90 inhibitors

Novobiocin analogs lacking labile glycosidic ether have been designed, synthesized and evaluated for Hsp90 inhibitory activity. Replacement of the synthetically complex noviose sugar with simple aromatic side chains produced analogs that maintain moderate cytotoxic activity against MCF7 and SkBR3 breast cancer cell-lines. Rationale for the preparation of des-noviose novobiocin analogs in addition to their synthesis and biological evaluation are presented herein.

High throughput discovery of heteroaromatic-modifying enzymes allows enhancement of novobiocin selectivity

Glycosylated analogues of novobiocin, discovered using a broad library of enzymes, have 100-fold improved activity against breast, brain, pancreatic, lung and ovarian cancers and ablated associated off-target activity leading to an up to 2.7 × 10(4) fold increase in selectivity.

The synthesis and evaluation of flavone and isoflavone chimeras of novobiocin and derrubone

The natural products novobiocin and derrubone have both demonstrated Hsp90 inhibition and structure-activity relationships have been established for each scaffold. Given these compounds share several key structural features, we hypothesized that incorporation of elements from each could provide insight to structural features important for Hsp90 inhibition. Thus, chimeric analogues of novobiocin and derrubone were constructed and evaluated. These studies confirmed that the functionality present at the 3-position of the isoflavone plays a critical role in determining Hsp90 inhibition and suggests that the bicyclic ring system present in both novobiocin and derrubone do not share similar modes of binding.

Synthesis and biological activity of simplified denoviose-coumarins related to novobiocin as potent inhibitors of heat-shock protein 90 (hsp90)

A new series of coumarin inhibitors of hsp90 lacking the noviose moiety as well as substituents on C-7 and C-8 positions of the aromatic ring was synthesised and their hsp90 inhibitory activity has been delineated: for example, their capacity to induce the degradation of client proteins and to inhibit estradiol-induced transcription in human breast cancer cells. In cell proliferation assay, the most active compound 5g was approximately 8 times more potent than the parent novobiocin natural compound.

Novobiocin: Redesigning a DNA Gyrase Inhibitor for Selective Inhibition of Hsp90

Novobiocin is a member of the coumermycin family of antibiotics and is a well-established inhibitor of DNA gyrase. Recent studies have shown that novobiocin binds to a previously unrecognized ATP-binding site at the C-terminus of Hsp90 and induces degradation of Hsp90-dependent client proteins at approximately 700 microM. In an effort to develop more efficacious inhibitors of the C-terminal binding site, a library of novobiocin analogues was prepared and initial structure-activity relationships revealed. These data suggested that the 4-hydroxy moiety of the coumarin ring and the 3'-carbamate of the noviose appendage were detrimental to Hsp90 inhibitory activity. In an effort to confirm these findings, 4-deshydroxy novobiocin (DHN1) and 3'-descarbamoyl-4-deshydroxynovobiocin (DHN2) were prepared and evaluated against Hsp90. Both compounds were significantly more potent than the natural product, and DHN2 proved to be more active than DHN1. In an effort to determine whether these moieties are important for DNA gyrase inhibition, these compounds were tested for their ability to inhibit DNA gyrase and found to exhibit significant reduction in gyrase activity. Thus, we have established the first set of compounds that clearly differentiate between the C-terminus of Hsp90 and DNA gyrase, converted a well-established gyrase inhibitor into a selective Hsp90 inhibitor, and confirmed essential structure-activity relationships for the coumermycin family of antibiotics.

Syntheses of photolabile novobiocin analogues

Novobiocin was recently shown to inhibit Hsp90 through a previously unrecognized C-terminal ATP binding site. Although the N-terminal region of Hsp90 has been solved by X-ray crystallography, the C-terminal region has not. In an effort to elucidate the C-terminal binding site of Hsp90, four photolabile analogues of novobiocin were prepared.

Synthesis of (−)-Noviose from 2,3-O-Isopropylidene-d-erythronolactol

Noviose is a key synthon for the construction of novobiocin, a clinically useful antitumor agent that has been shown to inhibit both type II topoisomerases and Hsp90. The synthesis of d-noviose from 2,3-O-isopropylidene-d-erythronolactol is described.

Antimicrobial and DNA gyrase-inhibitory activities of novel clorobiocin derivatives produced by mutasynthesis

Twenty-eight novel clorobiocin derivatives obtained from mutasynthesis experiments were investigated for their inhibitory activity towards Escherichia coli DNA gyrase and for their antibacterial activities towards clinically relevant gram-positive and gram-negative bacteria in comparison to novobiocin and clorobiocin. Clorobiocin was the most active compound both against E. coli DNA gyrase in vitro and against bacterial growth. All tested modifications of the 3-dimethylallyl-4-hydroxybenzoyl moiety reduced biological activity. The highest activities were shown by compounds containing a hydrophobic alkyl substituent at position 3 of the 4-hydroxybenzoyl moiety. Polar groups in this side chain, especially amide functions, strongly reduced antibacterial activity. Replacement of the alkyl side chain with a halogen atom or a methoxy group at the same position markedly reduced activity. Transfer of the pyrrole carboxylic acid moiety from O-3" to O-2" of L-noviose moderately reduced activity, whereas the complete absence of the pyrrole carboxylic acid moiety led to a loss of activity. Desclorobiocin derivatives lacking the chlorine atom at C-8 of the 3-amino-4,7-dihydroxycoumarin moiety also showed low activity. Lack of a methyl group at O-4" of L-noviose resulted in an inactive compound. From these findings it appears that clorobiocin represents a "highly evolved" structure optimized for bacterial transport and DNA gyrase inhibition.

D-Gulonolactone as a synthon for L-noviose: first preparation of 4-O-demethyl-L-noviofuranose and related derivatives

[reaction: see text] A new synthesis of L-noviose (11), a sugar moiety of novobiocin, is presented. D-Gulonolactone was initially converted in a few steps to the key ester derivative 7 [1-O-benzyl methyl 2,3-O-(1-methylethylidene)-alpha-L-lyxofuranosiduronate]. An appropriate selection of protecting groups enabled transformation of 7 under mild reaction conditions to 4-O-demethyl-L-noviofuranose 9a and related 9b-c. Derivatives 9 were further converted either to L-lyxopyranoses (10a and 10b) or to methyl L-lyxofuranoside 12.

Fine Tuning of physico-chemical parameters to optimise a new series of novobiocin analogues

A novel series of novobiocin analogues has been synthesised by removing the lipophilic aryl chain in novobiocin and introducing an amino substituent. The structural modifications have been dictated by the control of lipophilicity and the dissociation constant of the resulting compounds. Antibacterial activity of the new coumarin derivatives could be correlated with the amount of uncharged form in physiological conditions.

Novobiocin-related compounds: synthesis of 3-benzoylamino-2-oxo-2H-1-benzopyran-7-yl D-glycopyranosides by the trichloroacetimidate methodology

A general stereoselective method for the synthesis of 4-deoxynovobiocin-related glycosides is described. 3-Benzoylamino-2H-1-benzopyran-7-yl 2,3,4,6-tetra-O-acetyl-D-glycopyranosides of glucose, galactose and mannose were synthesised from appropriate O-glycosyltrichloroacetimidates and N-(7-hydroxy-2-oxo-2H-1-benzopyran-3-yl)benzamides in boiling methylene chloride in the presence of boron trifluoride etherate. Heating of these products in a mixture of triethylamine and methanol gave the corresponding deprotected 3-benzoylamino-2-oxo-2H-1-benzopyran-7-yl beta-D-glycopyranosides.

Synthesis of new fluidity-enhanced amphiphilic compounds for soluble protein two-dimensional crystallization purpose

The synthesis of new amphiphilic compounds is described. The structures are rationally designed for soluble protein two-dimensional (2D) crystallization purpose. Special attention is devoted to fluidity properties expected of resulting monolayers. A series of 13 compounds was prepared containing unsaturated, branched or fluorinated alkyl chains. Structures are either symmetrical or dissymmetrical and present a hydroxyl group as polar head, eventually complemented with two other 'secondary' hydrophilic functions.

Synthesis, antibacterial and antifungal activity of 4-hydroxycoumarin derivatives, analogues of novobiocin

3-Acylamino-, -arylsulfonylamino-, -(N'-arylureido)-, -arylideneamino- and -arylcarbamoyl-4-hydroxycoumarins have been synthesized and tested for antibacterial and antifungal activity. 3-Arylcarbamoyl-4-hydroxycoumarins have been shown to possess significant activity against Gram-positive bacteria; 3-acylamino-4-hydroxycoumarins have moderate antibacterial and antifungal effects whereas the additional compounds are inactive.

Correlation of hydrophobicity with protein binding for clorobiocin analogs

A new method of equilibrium dialysis was used to measure the binding of analogs of clorobiocin (18631 R.P.) to human serum albumin. Binding constants and numbers of binding sites on human serum albumin were calculated from the binding data and were used to calculate the percentage of compounds free in equilibrium with 4% albumin. Partition coefficients between n-octanol and phosphate buffer (0.05 M, pH 7.4) also were measured. A positive linear correlation (r = 0.918, s = 0.240, and n = 10) was obtained between log (bound/free compound) and log partition coefficient.