In vitro solubility assays in drug discovery

The solubility of a compound depends on its structure and solution conditions. Structure determines the lipophilicity, hydrogen bonding, molecular volume, crystal energy and ionizability, which determine solubility. Solution conditions are affected by pH, co-solvents, additives, ionic strength, time and temperature. Many drug discovery experiments are conducted under "kinetic" solubility conditions. In drug discovery, solubility has a major impact on bioassays, formulation for in vivo dosing, and intestinal absorption. A good goal for the solubility of drug discovery compounds is >60 ug/mL. Equilibrium solubility assays can be conducted in moderate throughput, by incubating excess solid with buffer and agitating for several days, prior to filtration and HPLC quantitation. Kinetic solubility assays are performed in high throughput with shorter incubation times and high throughput analyses using plate readers. The most frequently used of these are the nephelometric assay and direct UV assay, which begin by adding a small volume of DMSO stock solution of each test compound to buffer. In nephelometry, this solution is serially diluted across a microtitre plate and undissolved particles are detected via light scattering. In direct UV, undissolved particles are separated by filtration, after which the dissolved material is quantitated using UV absorption. Equilibrium solubility is useful for preformulation. Kinetic solubility is useful for rapid compound assessment, guiding optimization via structure modification, and diagnosing bioassays. It is often useful to customize solubility experiments using conditions that answer specific research questions of drug discovery teams, such as compound selection and vehicle development for pharmacology and PK studies.

Practice Parameter: evaluation of distal symmetric polyneuropathy: role of autonomic testing, nerve biopsy, and skin biopsy (an evidence-based review). Report of the American Academy of Neurology, American Association of Neuromuscular and Electrodiagnostic Medicine, and American Academy of Physical Medicine and Rehabilitation

BACKGROUND

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence-based guidelines regarding the role of autonomic testing, nerve biopsy, and skin biopsy for the assessment of polyneuropathy.

METHODS

A literature review using MEDLINE, EMBASE, and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four-tiered level of evidence scheme and recommendations were based upon the level of evidence.

RESULTS AND RECOMMENDATIONS

1) Autonomic testing should be considered in the evaluation of patients with polyneuropathy to document autonomic nervous system dysfunction (Level B). Such testing should be considered especially for the evaluation of suspected autonomic neuropathy (Level B) and distal small fiber sensory polyneuropathy (SFSN) (Level C). A battery of validated tests is recommended to achieve the highest diagnostic accuracy (Level B). 2) Nerve biopsy is generally accepted as useful in the evaluation of certain neuropathies as in patients with suspected amyloid neuropathy, mononeuropathy multiplex due to vasculitis, or with atypical forms of chronic inflammatory demyelinating polyneuropathy (CIDP). However, the literature is insufficient to provide a recommendation regarding when a nerve biopsy may be useful in the evaluation of DSP (Level U). 3) Skin biopsy is a validated technique for determining intraepidermal nerve fiber density and may be considered for the diagnosis of DSP, particularly SFSN (Level C). There is a need for additional prospective studies to define more exact guidelines for the evaluation of polyneuropathy.

Investigating the biosynthetic origin of the nitro group in pyrrolomycins

Feasible modes of introducing the nitro group into pyrrolomycin antibiotics were investigated based on incorporation of (15)N-labeled arginine and proline into dioxapyrrolomycin, produced by the actinomycete culture LL-F42248. Biosynthesis of nitrated pyrrolomycins was unaffected by the presence of nitric oxide synthase (NOS) inhibitors. The culture was able to grow in nitrogen-free (minimal) media and produce nitrated secondary metabolites. These results indicate that LL-F42248 is capable of fixing nitrogen.

Biosynthesis of diazepinomicin/ECO-4601, a Micromonospora secondary metabolite with a novel ring system

The novel microbial metabolite diazepinomicin/ECO-4601 (1) has a unique tricyclic dibenzodiazepinone core, which was unprecedented among microbial metabolites. Labeled feeding experiments indicated that the carbocyclic ring and the ring nitrogen of tryptophan could be incorporated via degradation to the 3-hydroxyanthranilic acid, forming ring A and the nonamide nitrogen of 1. Genomic analysis of the biosynthetic locus indicated that the farnesyl side chain was mevalonate derived, the 3-hydroxyanthranilic acid moiety could be formed directly from chorismate, and the third ring was constructed via 3-amino-5-hydroxybenzoic acid. Successful incorporation of 4,6-D2-3-hydroxyanthranilic acid into ring A of 1 via feeding experiments supports the genetic analysis and the allocation of the locus to this biosynthesis. These studies highlight the enzymatic complexity needed to produce this structural type, which is rare in nature.

Late-onset hereditary axonal neuropathies

BACKGROUND

Hereditary motor-sensory neuropathy or the Charcot-Marie-Tooth syndrome is known to represent considerable genetic heterogeneity. Onset is usually in childhood, adolescence, or young adulthood. The objective of this study was to define late-onset forms of the disorder.

METHODS

A clinical and genetic study of families with uniformly late onset of peripheral neuropathy was performed in a university neurogenetics setting.

RESULTS

Six families were identified with consistently late onset of a primarily axonal neuropathy. Median age at symptom onset was 57 years (range 35-85 years) of a mixed motor and sensory neuropathy with electrophysiologic characteristics of an axonal rather than demyelinating condition. There was a possible association with deafness. Two families showed autosomal dominant inheritance whereas four families had only one affected generation with an excess of males. An extensive mutation screen of nine genes known to cause Charcot-Marie-Tooth was negative.

CONCLUSIONS

There are late-onset forms of hereditary axonal neuropathies. The genetic causes remain unknown and genetic heterogeneity within this entity is likely.

Reassessing the structure of pyranonigrin

Fermentation extracts of the marine fungus Aspergillus niger LL-LV3020 were found to have relevant activity in a number of assays. Chemical screening of the extracts revealed that this organism produced numerous secondary metabolites in addition to its principal metabolite, citric acid. The compound with the most significant UV peak was isolated and its structure elucidated. Physical data suggested that this compound is identical with pyranonigrin A (1); however, our structure elucidation led to a different assignment than previously reported. On the basis of analysis of all data, we propose a correction to the structure of pyranonigrin A. Its absolute configuration was determined by electronic circular dichroism measurements in comparison with theoretical values calculated via ab initio time-dependent density functional theory and assigned as (7R)-3,7-dihydroxy-2-[(1E)-prop-1-enyl]-6,7-dihydropyrano[2,3-c]pyrrole-4,5-dione.

Comparison of cytochrome P450 inhibition assays for drug discovery using human liver microsomes with LC–MS, rhCYP450 isozymes with fluorescence, and double cocktail with LC–MS

The disparity of IC(50)s from CYP450 inhibition assays used to assess drug-drug interaction potential was investigated, in order to have evidence for selecting a reliable in vitro CYP450 inhibition assay to support drug discovery. Three assays were studied: individual rhCYP isozymes and corresponding coumarin derivative-probe substrates with fluorescent detection, human liver microsomes (HLM) and cocktail drug-probe substrates with LC-MS detection, and double cocktail rhCYP isozymes mix and drug-probe mix with LC-MS detection. Data comparisons showed that the rhCYP-fluorescent assay and the cocktail assay with HLM-LC-MS had weak correlation. Detection method and probe substrates were shown to not be the major cause of the disparity in IC(50)s. However, the enzyme source and composition (HLM versus, rhCYP) caused disparity in IC(50)s. Specifically, the high concentrations of CYP isozymes often used with HLM-based assays produced high probe substrate conversion and test compound metabolism, which should both contribute to artificially higher IC(50)s. Non-specific binding of substrate to higher concentration proteins and lipids in the HLM-based assays should also contribute to higher IC(50)s. The modified double cocktail assay was found to overcome limitations of the other two assays. It uses an rhCYP isozymes mix, drug-probe substrate mix, low protein concentration, and LC-MS detection. The double cocktail assay is sensitive, selective, and high throughout for use in drug discovery to provide an early alert to potential toxicity with regard to drug-drug interaction, prioritize chemical series, and guide structural modification to circumvent CYP450 inhibition.

Structure and absolute stereochemistry of 21-hydroxyoligomycin A

21-Hydroxyoligomycin A (1) was isolated from Streptomyces cyaneogriseus ssp. noncyanogenus (LL-F28249) and fully characterized by NMR and single-crystal X-ray diffraction methods. The complete 1H and 13C NMR chemical shift assignments for 1 were made using 2D NMR experiments, and the chirality at C-21 was deduced to be R from a J-based configuration analysis. The absolute configuration at C-21 and at the other 18 chiral centers in the molecule were independently confirmed by anomalous dispersion measurements on a crystal of the chloroform methanol solvate of 21-hydroxyoligomycin A (1).

Septocylindrins A and B: peptaibols produced by the terrestrial fungus Septocylindrium sp. LL-Z1518

Two new peptaibols, septocylindrin A (1) and septocylindrin B (2), related to the well-studied membrane-channel-forming peptaibol alamethicin, were obtained from a terrestrial isolate of the fungus Septocylindrium sp. Both 1 and 2 are linear 19-amino acid peptides with a modified phenylalanine C-terminus. Analysis of the HRMS data indicated that they differ only in the 18th residue, where 1 contains Glu and 2 contains Gln. The structures of these two peptaibols were determined by extensive NMR and HRMS analysis. The absolute configurations of amino acids present in 1 were determined using Marfey's methodology. Both compounds were isolated through bioassay-guided fractionation and exhibited significant antibacterial and antifungal activity.

Direct high-performance liquid chromatographic separation of the enantiomers of an aromatic amine and four aminoalcohols using polysaccharide chiral stationary phases and acidic additive

The HPLC enantiomeric separation of N-benzyl-alpha-methyl-benzylamine, phenylalaninol, tryptophanol, 2 (diphenylhydroxymethyl)pyrrolidine, and isoproterenol was accomplished in the normal-phase mode using two polysaccharide-derived chiral stationary phases (CSPs) and various n-hexane/2-propanol mobile phases with acidic (TFA) or basic (DEA) additive. The compounds were separated without any derivatization and separation factor range between 2.09 and 1.09 with resolution factor 3.4 and 0.4, respectively. The best separation of the enantiomers of the amine was achieved on amylose tris (3, 5-dimethylphenylcarbamate) CSP with TFA additive in the mobile phase; in acidic conditions, instead, the best enantioseparation of the aminoalcohols was achieved on cellulose tris (3, 5-dimethylphenilcarbamate). A long equilibration time of the CSP when switching from an undoped mobile phase to a doped one is required to obtain reproducible results.

Dioxapyrrolomycin biosynthesis in Streptomyces fumanus

Streptomyces fumanus, intramurally coded as culture LL-F42248, produces a series of pyrrolomycins including dioxapyrrolomycin (1) as the principal component. Our biosynthetic studies revealed that feeding labeled acetate to growing cultures of S. fumanus yielded pyrrolomycins labeled in the phenyl ring only. When l-[methyl-13C]methionine was fed, the labeled carbon atom was found in the methoxy group of pyrrolomycins H-J and in the methylenedioxy bridge of dioxapyrrolomycin. A Na15NO3-enriched medium was employed to produce 15N-labeled pyrrolomycins in which both nitrogen atoms were highly enriched, whereas feeding of 15N-labeled l-proline furnished pyrrolomycins labeled in the pyrrole moiety. Thus, S. fumanus elaborates the pyrrolomycin skeleton from proline and a polyketide precursor. Since the organism readily converted 13C- or 15N-labeled pyrrolomycin C, G, or H into the correspondingly labeled dioxapyrrolomycin, these minor pyrrolomycins are actually precursors of the ultimate product, dioxapyrrolomycin.

Hygrocins a and B, naphthoquinone macrolides from Streptomyces hygroscopicus

Two new naphthoquinone macrolides, hygrocins A (1) and B (2), were isolated from the fermentation broth of Streptomyces hygroscopicus. Hygrocin A is not stable due to the presence of an active methylene group (C-22), which undergoes intramolecular aldol condensation with the quinone ring to yield a gamma-lactam derivative, 6. Its structural elucidation was achieved by chemical conversion to 3, an unusual diazomethane derivative, and confirmed by its alkaline hydrolysis product 4, hydrogenation derivative 5, and "degradation" product 6. The structure of hygrocin B was determined by combined chemical and spectroscopic methods.

Distal symmetric polyneuropathy: a definition for clinical research: report of the American Academy of Neurology, the American Association of Electrodiagnostic Medicine, and the American Academy of Physical Medicine and Rehabilitation

The objective of this report was to develop a case definition of distal symmetric polyneuropathy to standardize and facilitate clinical research and epidemiologic studies. A formalized consensus process was employed to reach agreement after a systematic review and classification of evidence from the literature. The literature indicates that symptoms alone have relatively poor diagnostic accuracy in predicting the presence of polyneuropathy; signs are better predictors of polyneuropathy than symptoms; and single abnormalities on examination are less sensitive than multiple abnormalities in predicting the presence of polyneuropathy. The combination of neuropathic symptoms, signs, and electrodiagnostic findings provides the most accurate diagnosis of distal symmetric polyneuropathy. A set of case definitions was rank ordered by likelihood of disease. The highest likelihood of polyneuropathy (useful for clinical trials) occurs with a combination of multiple symptoms, multiple signs, and abnormal electrodiagnostic studies. A modest likelihood of polyneuropathy (useful for field or epidemiologic studies) occurs with a combination of multiple symptoms and multiple signs when the results of electrodiagnostic studies are not available. A lower likelihood of polyneuropathy occurs when electrodiagnostic studies and signs are discordant. For research purposes, the best approach to defining distal symmetric polyneuropathy is a set of case definitions rank ordered by estimated likelihood of disease. The inclusion of this formalized case definition in clinical and epidemiologic research studies will ensure greater consistency of case selection.

Production of novel rapamycin analogs by precursor-directed biosynthesis

The natural product rapamycin, produced during fermentation by Streptomyces hygroscopicus, is known for its potent antifungal, immunosuppressive, and anticancer activities. During rapamycin biosynthesis, the amino acid l-pipecolate is incorporated into the rapamycin molecule. We investigated the use of precursor-directed biosynthesis to create new rapamycin analogs by substitution of unusual l-pipecolate analogs in place of the normal amino acid. Our results suggest that the l-pipecolate analog (+/-)-nipecotic acid inhibits the biosynthesis of l-pipecolate, thereby limiting the availability of this molecule for rapamycin biosynthesis. We used (+/-)-nipecotic acid in our precursor-directed biosynthesis studies to reduce l-pipecolate availability and thereby enhance the incorporation of other pipecolate analogs into the rapamycin molecule. We describe here the use of this method for production of two new sulfur-containing rapamycin analogs, 20-thiarapamycin and 15-deoxo-19-sulfoxylrapamycin, and report measurement of their binding to FKBP12.

Pseudopyronines A and B, alpha-pyrones produced by a marine Pseudomonas sp. F92S91, and evidence for the conversion of 4-hydroxy-alpha-pyrone to 3-furanone

In our search for inhibitors of bacterial fatty acid biosynthesis, two new alpha-pyrones, pseudopyronines A (1) and B (2), were isolated from a marine Pseudomonas sp. F92S91. The naturally occurring alpha-pyrones appeared to be unstable, evidenced by the conversion of pseudopyronine B into an oxidation product, 3-furanone (3). Structural elucidations were made by spectroscopic analyses including 2D-NMR data.

Fumaquinone, a New Prenylated Naphthoquinone from Streptomyces fumanus

A new prenylated naphthoquinone antibiotic, fumaquinone (5,7-dihydroxy-2-methoxy-3-methyl-6-(3-methyl-but-2-enyl)[1,4]naphthoquinone) was isolated from cultures of Streptomyces fumanus (LL-F42248). Its chemical structure was determined primarily by NMR spectroscopy. Preliminary feeding experiments indicated the naphthoquinone is of polyketide origin, while the O-methyl and aromatic C-methyl groups are derived from methionine.

Rediscovering natural products as a source of new drugs

Extract: Since the very beginnings of human medicine, physicians have relied on chemical compounds produced by animals, plants and microorganisms, so-called natural products, to treat diseases. Natural products are directly or indirectly responsible for roughly one-half of all drugs currently in use. Of the 877 small-molecule new drug molecules introduced between 1981 and 2002, 49% were natural products or natural product analogs. Despite the great success of the 70s and 80s, the pharmaceutical industry de-emphasized natural products research during the following decade. In this article, we examine the underlying reasons for the decline, and assess future prospects for natural products research in drug discovery. In the 1990s, major pharmaceutical companies moved to a lead-finding strategy based on High Throughput Screening (HTS) of very large collections (libraries) of synthetic compounds. The move arose from the belief that techniques such as combinatorial chemistry could produce larger, more cost-effective libraries with improved hit rates and quality. Additionally, advances in molecular biology, cellular biology and genomics dramatically increased the number of molecular targets, prompting shorter drug discovery timelines. In today's drug discovery environment, rapid screening and identification of potential drug molecules is essential for success. This puts traditional natural products-based programs, with their reliance on the lengthy processes of the screening of extracts library, bioassay-guided isolation of the active components, structure elucidation and subsequent production scale-up, at a competitive disadvantage.

The evolving role of natural products in drug discovery

Natural products and their derivatives have historically been invaluable as a source of therapeutic agents. However, in the past decade, research into natural products in the pharmaceutical industry has declined, owing to issues such as the lack of compatibility of traditional natural-product extract libraries with high-throughput screening. However, as discussed in this review, recent technological advances that help to address these issues, coupled with unrealized expectations from current lead-generation strategies, have led to a renewed interest in natural products in drug discovery.

Additional pyrrolomycins from cultures of Streptomyces fumanus

Along with dioxapyrrolomycin (1), four new pyrrolomycin antibiotics, namely, pyrrolomycin G (3), pyrrolomycin H (4), pyrrolomycin I (5), and pyrrolomycin J (6), were produced in cultures of Streptomyces fumanus. Apart from dioxapyrrolomycin, pyrrolomycin G and pyrrolomycin H are the only other chiral members of the pyrrolomycin family of antibiotics, and their absolute stereochemistry was deduced to be 13S. Here, we report the isolation, structure elucidation, and antimicrobial activity of these new pyrrolomycins.

07H239-A, a new cytotoxic eremophilane sesquiterpene from the marine-derived Xylariaceous fungus LL-07H239

07H239-A (1), a new eremophilane sesquiterpene from a marine-derived xylariaceous fungus, was isolated, characterized, and shown to be cytotoxic toward a variety of cancer cell lines, with some selectivity for a CCRFCEM leukemia line (IC(50) = 0.9 microg/mL).

Diazepinomicin, a new antimicrobial alkaloid from a marine Micromonospora sp

The structure of a new dibenzodiazepine alkaloid, diazepinomicin (1), isolated from the culture of a marine actinomycete of the genus Micromonospora was characterized using spectroscopic methods. Diazepinomicin represents a unique molecular class composed of a dibenzodiazepine core linked to a farnesyl side chain.

Dictyosphaeric acids A and B: new decalactones from an undescribed Penicillium sp. obtained from the alga Dictyosphaeria versluyii

Fungal isolate F01V25 was obtained from the alga Dictyosphaeria versluyii collected near Dravuni, Fiji, in 2001 and represented a previously undescribed Penicillium sp. Fermentation of isolate F01V25 resulted in the production of two new polyketides, dictyosphaeric acids A and B, along with the known anthraquinone carviolin. The relative stereochemistry of dictyosphaeric acids A and B was determined using the J-based configuration analysis method in conjunction with ROE and NOE correlations.

Microcionamides A and B, Bioactive Peptides from the Philippine Sponge Clathria (Thalysias) abietina

Microcionamides A (1) and B (2) have been isolated from the Philippine marine sponge Clathria (Thalysias) abietina. These new linear peptides are cyclized via a cystine moiety and have their C-terminus blocked by a 2-phenylethylenamine group. Their total structures, including absolute stereochemistry, were determined by a combination of spectral and chemical methods. Compound 1 was shown to slowly isomerize about the C-36/C-37 double bond when stored in DMSO. Microcionamides A (1) and B (2) exhibited significant cytotoxicity against the human breast tumor cells lines MCF-7 and SKBR-3 and displayed inhibitory activity against Mycobacterium tuberculosis H(37)Ra.