Johan Gottfries

Assessing the performance of OMEGA with respect to retrieving bioactive conformations

OMEGA is a rule-based program which rapidly generates conformational ensembles of small molecules. We have varied the parameters which control the nature of the ensembles generated by OMEGA in a statistical fashion (D-optimal) with the aim of increasing the probability of generating bioactive conformations. Thirty-six drug-like ligands from different ligand-protein complexes determined by high-resolution (< or =2.0A) X-ray crystallography have been analyzed. Statistically significant models (Q(2)> or =0.75) confirm that one can increase the performance of OMEGA by modifying the parameters. Twenty-eight of the bioactive conformations were retrieved when using a low-energy cut-off (5 kcal/mol), a low RMSD value (0.6A) for duplicate removal, and a maximum of 1000 output conformations. All of those that were not retrieved had eight or more rotatable bonds. The duplicate removal parameter was found to have the largest impact on retrieval of bioactive conformations, and the maximum number of conformations also affected the results considerably. The input conformation was found to influence the results largely because certain bond angles can prevent the bioactive conformation from being generated as a low-energy conformation. Pre-optimizing the input structures with MMFF94s improved the results significantly. We also investigated the performance of OMEGA in connection with database searching. The shape-matching program Rapid Overlay of Chemical Structures (ROCS) was used as search tool. Two multi-conformational databases were built from the MDDR database plus the 36 compounds; one large (maximum 1000 conformations/mol) and one small (maximum 100 conformations/mol). Both databases provided satisfactory results in terms of retrieval. ROCS was able to rank 35 out of 36 X-ray structures among the top 500 hits from the large database.

Sensitivity, specificity, and stability of CSF-tau in AD in a community-based patient sample

OBJECTIVEnTo evaluate the sensitivity and specificity of CSF-tau in clinical practice as a diagnostic marker for AD compared with normal aging and depression, to study the stability of CSF-tau in longitudinal samples, and to determine whether CSF-tau levels are influenced by different covariates such as gender, age, duration or severity of disease, or possession of the APOE-epsilon4 allele.nnnMETHODSnConsecutive AD patients from a community-based sample were studied, including 407 patients with AD (274 with probable AD and 133 with possible AD), 28 patients with depression, and 65 healthy elderly control subjects. A follow-up lumbar puncture was performed in 192 AD patients after approximately 1 year. CSF-tau was determined using a sandwich ELISA, which was run as a routine clinical neurochemical analysis.nnnRESULTSnCSF-tau was increased in probable (690+/-341 pg/mL; p < 0.0001) and possible (661+/-447 pg/mL; p < 0.0001) AD, but not in depression (231+/-110 pg/mL) compared with control subjects (227+/-101 pg/mL). Receiver operating characteristics analysis showed that a cutoff level of 302 pg/mL resulted in a sensitivity of 93% (95% CI, 90-96%) and a specificity of 86% (95% CI, 75-94%), with an area under the curve of 0.95 to discriminate AD from control subjects. Within the AD group, CSF-tau did not differ significantly between baseline and follow-up investigations, and was relatively stable between baseline and 1-year follow-up levels, with a coefficient of variation of 21.0%. High CSF-tau levels were also found in most AD patients with very short duration of dementia, and with Mini-Mental State Examination scores >23 (n = 205). In total, 193 of 205 patients (sensitivity, 94%) had a CSF-tau level higher than 302 pg/mL.nnnCONCLUSIONSnCSF-tau has a high sensitivity and specificity to differentiate AD from normal aging and depression, as demonstrated in a large community-based series of consecutive AD patients during which analyses were run continually in a clinical neurochemical laboratory. The increase in CSF-tau is found very early in the disease process in AD, is stable over time, and has a low interindividual variation on repeated sampling. Although high CSF-tau is found in some neurologic conditions (e.g., stroke), these findings suggest that CSF-tau may be of use to help in differentiating AD from normal aging and depression, especially early in the course of the disease, when the symptoms are vague and the diagnosis is especially difficult.

Lack of replication of association findings in complex disease: an analysis of 15 polymorphisms in prior candidate genes for sporadic Alzheimer's disease

There is considerable enthusiasm for the prospect of using common polymorphisms (primarily single nucleotide polymorphisms; SNPs) in candidate genes to unravel the genetics of complex disease. This approach has generated a number of findings of loci which are significantly associated with sporadic Alzheimers disease (AD). In the present study, a total of 15 genes of interest were chosen from among the previously published reports of significant association in AD. Genotyping was performed on polymorphisms within those genes (14 SNPs and one deletion) using Dynamic Allele Specific Hybridization (DASH) in 204 Swedish patients with sporadic late-onset AD and 186 Swedish control subjects. The genes chosen for analysis were; low-density lipoprotein receptor-related protein (LRP1), angiotensin converting enzyme (DCP1), alpha-2-macroglobulin (A2M), bleomycin hydrolase (BLMH), dihydrolipoyl S-succinyltransferase (DLST), tumour necrosis factor receptor superfamily member 6 (TNFRSF6), nitric oxide synthase (NOS3), presenilin 1 (PSEN1), presenilin 2 (PSEN2), butyrylcholinesterase (BCHE), Fe65 (APBB1), oestrogen receptor alpha (ESR1), cathepsin D (CTSD), methylenetetrahydrofolate reductase (MTHFR), and interleukin 1A (IL1A). We found no strong evidence of association for any of these loci with AD in this population. While the possibility exists that the genes analysed are involved in AD (ie they have weak effects and/or are population specific), results reinforce the need for extensive replication studies if we are to be successful in defining true risk factors in complex diseases.

Identification of CSF biomarkers for frontotemporal dementia using SELDI-TOF

This investigation describes the discovery of novel possible cerebrospinal fluid (CSF) biomarkers for frontotemporal dementia (FTD) using surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS). Sixteen clinically diagnosed FTD patients and 12 non-demented controls were included in the study. CSF was collected and analyzed for protein expression by SELDI-TOF MS. The samples were analyzed on four different array surfaces using two different energy-absorbing molecules as matrices. In total each sample was subjected to eight different surface/matrix conditions. About 2000 protein peaks (mass/charge ratios) were detected. Forty-two peaks were differentially expressed in FTD (P < 0.01). After exclusion of peaks with low signal-to-noise ratio and/or poor resolution and peaks representing differentially charged proteins, 10 peaks remained, five of which were increased and five decreased in FTD cases compared to controls. Using partial least square discriminant analysis (PLS-DA), the combination of these biomarkers discriminated FTD from non-demented controls with a sensitivity of 94%, a specificity of 83% and an accuracy of 89%. Five of the peaks were purified further and identified by tandem MS as a fragment of neurosecretory protein VGF, transthyretin, S-cysteinylated transthyretin, truncated cystatin C and a fragment of chromogranin B. With use of these potential biomarkers, FTD can be distinguished from control subjects with high accuracy in this pilot study.

Toward minimalistic modeling of oral drug absorption

Poor intestinal permeability of drugs constitutes a major bottleneck in the successful development of candidate drugs. Fast computational tools to help in designing compounds with increased probability of oral absorption are required, since both medicinal and combinatorial chemists are under pressure to consider increasing numbers of virtual and existing compounds. The QSAR paradigm for drug absorption is expressed as a function of molecular size, hydrogen-bonding capacity, and lipophilicity. A nonlinear PLS model that can be achieved with minimal computational efforts is described. The QSAR model correlates human intestinal absorption (%HIA) data, and apparent Caco-2 cell permeability data, to parameters calculated from molecular structures. Two properties were found to be relevant for absorption predictions, namely H-bonding capacity, and hydrophobic transferability. The parsimony principle was applied in several aspects: single conformers were used to compute molecular surface areas; the definitions of polar and nonpolar surfaces were done in a simplistic fashion; simple and fast 2D descriptors were used to estimate other properties; the 1 PLS component model was selected. These choices result in a minimalistic model for oral absorption. The use of both %HIA and Caco-2 permeability data was found to stabilize and improve the model. This QSAR model can serve as a simple, quantitative extension of the rule of five scheme (Lipinski, C.A., Lombardo, F., Dominy, B.W., and Feeney, P.J. Adv. Drug Deliv. Rev. 1997, 23, 3-25), in a manner that can prove beneficial to the drug discovery process.

The Cerebrospinal Fluid Levels of Tau, Growth-Associated Protein-43 and Soluble Amyloid Precursor Protein Correlate in Alzheimer’s Disease, Reflecting a Common Pathophysiological Process

Cerebrospinal fluid (CSF) levels of tau (total tau), growth-associated protein-43 (GAP-43), soluble amyloid precursor protein (sAPP; i.e. total sAPP), and β-amyloid42 (Aβ42) were studied in patients with frontotemporal dementia (FTD; n = 14), Alzheimer’s disease (AD; n = 47) and vascular dementia (VAD; n = 16), and in age-matched controls (n = 12). CSF-tau was increased in AD compared to controls and FTD (p < 0.001 for both). CSF-GAP-43 was increased in AD compared to controls (p < 0.05), and both CSF-GAP-43 and CSF-sAPP were increased in AD compared to FTD (p < 0.01). Positive and highly significant correlations were found between CSF-tau and CSF-GAP-43 in all groups and between CSF-tau, CSF-GAP-43 and CSF-sAPP in AD. The correlations found may reflect a common pathophysiologic process such as axonal degeneration.

Cerebrospinal fluid phospho-tau, total tau and beta-amyloid(1-42) in the differentiation between Alzheimer's disease and vascular dementia.

The two most frequently examined biomarkers in the diagnosis of dementia are cerebrospinal fluid (CSF) tau and β-amyloid1–42 (Aβ1–42). An assay for tau phosphorylated at threonine 181 (phospho-tau) has recently been developed. We studied these three markers in patients with possible Alzheimer’s disease (AD; n = 23), probable AD (n = 50), AD with relevant cerebrovascular disease (AD with CVD; n = 14), possible vascular dementia (VaD; n = 39), probable VaD (n = 36), cognitively impaired (n = 13) and 27 neurologically healthy controls. Compared with the controls, tau levels were significantly increased in possible AD, probable AD, AD with CVD and probable VaD. Aβ1–42 was decreased in all dementia groups compared with the controls. In contrast, phospho-tau levels were increased only in probable AD compared with the controls. From the results of the present study, it is concluded that neither measurement of phospho-tau, tau nor Aβ1–42 in CSF can discriminate entirely between dementia and cognitively non-disturbed controls or between dementia of different aetiologies in the clinical diagnostic procedure.

Label-free primary screening and affinity ranking of fragment libraries using parallel analysis of protein panels.

The authors present fragment screening data obtained using a label-free parallel analysis approach where the binding of fragment library compounds to 4 different target proteins can be screened simultaneously using surface plasmon resonance detection. They suggest this method as a first step in fragment screening to identify and select binders, reducing the demanding requirements on subsequent X-ray or nuclear magnetic resonance studies, and as a valuable “clean-up” tool to eliminate unwanted promiscuous binders from libraries. A small directed fragment library of known thrombin binders and a general 500-compound fragment library were used in this study. Thrombin, blocked thrombin, carbonic anhydrase, and glutathione-S-transferase were immobilized on the sensor chip surface, and the direct binding of the fragments was studied in real time. Only 12 µg of each protein is needed for screening of a 3000-compound fragment library. For screening, a binding site-blocked target as reference facilitates the identification of binding site-selective hits and the signals from other reference proteins for the elimination of false positives. The scope and limitations of this screening approach are discussed for both target-directed and general fragment libraries. (Journal of Biomolecular Screening 2008:202-209)

Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces

Abstract Structure-property relationships, central to many of today’s drug discovery strategies, are not straightforward to deal with when trying to predict drug efficacy, that is, the combined outcome of target affinity, pharmacodynamic behavior, pharmacokinetic properties, and metabolic fate. In this article, we discuss the handling of chemical property information in reagents-for-synthesis selection, enumeration, and virtual library construction. We describe the use of diversity assessment and/or experimental design in selection of compound-libraries-to-be-synthesized. Our overall objective was to identify good-quality drug candidates through reliable structure-activity relationship data, with the minimum number of compounds synthesized and tested. Chemical filters, property filters, scoring functions, and utilization of interactive visualization tools are discussed. The concept of chemical diversity and aspects of chemical space navigation employing a proprietary tool, Chemical Global Positioning System (ChemGPS), for mapping the drug-related chemical space are examined. Guidelines and workflow recommendations for the practicing medicinal chemist are proposed.

One-Carbon Metabolism and Other Biochemical Correlates of Cognitive Impairment as Visualized by Principal Component Analysis

In the present report, 101 ambulatory elderly patients complaining about cognitive disturbances were investigated using the Mini-Mental State Examination (MMSE). Laboratory investigations, brain imaging, and electroen cephalography were performed. Twelve patients were diagnosed with subjective memory complaints (SMC), 32 with mild cognitive impairment (MCI), 43 with dementia of the Alzheimer type (DAT), and 14 with vascular dementia (VAD). Thirty-three percent of the SMC group, 31% of the MCI group, 45% of the DAT group, and 62% of the VAD group had increased serum homocysteine (s-HCY). Principal component analysis of 19 variables showed 3 signifi cant principal components by cross-validation. The cognitive impairment in the patients (MMSE) was explained to 50%. According to the principal component analysis, the population followed two different routes to cognitive impair ment : one correlated with disturbance of one-carbon metabolism (cerebrospinal fluid vitamin B12, plasma B12, plasma folate, and s-HCY) and the other correlated with more classic dementia, as marked by cerebrospinal fluid tau, vas cular risk factors, atrophy on brain imaging, possession of the apolipoprotein E4 allele, and age. There was poor discrimination between DAT and VAD. (J Geriatr Psychiatry Neurol 2001; 14:109-114).