Comparative binding energy (COMBINE) analysis of human neutrophil elastase inhibition by pyridone-containing trifluoromethylketones

The complexes of human neutrophil elastase with a series of 40 N3-substituted trifluoromethylketone-based pyridone inhibitors have been modelled. The series spans three orders of magnitude in inhibition constants despite the fact that it was originally developed in an attempt to improve the oral activity of a lead compound. Ligand-receptor interaction energies calculated using molecular mechanics did not correlate well with the experimental activities. A good correlation with activity was found, however, when a COMBINE analysis of the same data was carried out, which allowed a quantitative interpretation of the modelled complexes. The essence of this method is to partition the ligand-receptor interaction energies into individual residue-based van der Waals and electrostatic contributions, and to subject the resulting energy matrix to partial least squares analysis. Incorporation of two additional descriptors representing the electrostatic energy contributions to the partial desolvation of both the receptor and the ligands improved the QSAR model, as did the replacement of the distance-dependent electrostatic contributions with solvent-screened electrostatic interactions calculated by numerically solving the Poisson-Boltzmann equation. The model was validated both internally (cross-validation) and externally, using a set of twelve 6-phenyl-pyridopyrimidine analogs. The analysis reveals the subtle interplay of binding forces which occurs within the enzyme active site and provides objective information that can be interpreted in the light of the receptor structure. This information, gained from a series of real compounds, can be easily translated into 3D real or virtual database queries in the search for more active derivatives.

De novo hepatitis B after liver transplantation from hepatitis B core antibody-positive donors in an area with high prevalence of anti-HBc positivity in the donor population

Transmission of hepatitis B virus (HBV) infection from donors who are negative for hepatitis B surface antigen (HBsAg-) but positive for antibody to hepatitis B core antigen (anti-HBc+) has been reported. However, previous studies were generally performed in geographic regions with a low prevalence of anti-HBc positivity in the liver donor population. The aims of this study are (1) to assess the risk for de novo hepatitis B in recipients of livers from anti-HBc+ donors in an area of high prevalence of anti-HBc positivity in the donor population, and (2) to analyze the risk factors for acquisition of HBV infection from anti-HBc+ donors. The transplantation experience of a single center between 1995 and 1998 was reviewed. Thirty-three of 268 liver donors (12%) were HBsAg- and anti-HBc+ during the study period. The proportion of anti-HBc+ donors increased with age; it was lowest (3.6%) in donors aged 1 to 20 years and highest (27.1%) in donors aged older than 60 years. Of the 211 HBsAg- recipients with 3 months or more of HBV serological follow-up, 30 received a liver from an anti-HBc+ donor and 181 received a liver from an anti-HBc- donor. Hepatitis B developed in 15 of 30 recipients (50%) of livers from anti-HBc+ donors but in only 3 of 181 recipients (1.7%) of livers from anti-HBc- donors (P < .0001). None of the 4 recipients who were antibody to HBsAg (anti-HBs)+ at the time of transplantation developed HBV infection after receiving a liver from an anti-HBc+ donor compared with 15 of 26 recipients (58%) who were anti-HBs- (P =.10). None of the 5 anti-HBc+ recipients developed hepatitis B compared with 15 of 25 anti-HBc- recipients (60%; P = 0.04). Child-Pugh score was significantly higher in recipients of livers from anti-HBc+ donors who developed HBV infection than in those who did not (9 +/- 2 v 7 +/- 1; P =.03). In our area, testing liver donors for anti-HBc is mandatory, particularly in older donors. With such information available, anti-HBc+ donors can be safely directed to appropriate recipients, mainly those with anti-HBs and/or anti-HBc at the time of transplantation. In the current era of donor shortage, this policy would allow adequate use of such donors.

VolSurf: a new tool for the pharmacokinetic optimization of lead compounds

A method for the modeling and prediction of pharmacokinetic properties based on computed molecular interaction fields and multivariate statistics has been investigated in different experimental datasets. The program VolSurf was used to correlate 3D molecular structures with physico-chemical and pharmacokinetic properties. In membrane partitioning, VolSurf produced a two-component model explaining 94% of the total variation with a predictive q(2) of 0.90. This result was achieved without conformational sampling and without any quantum-chemical calculation. For the prediction of blood-brain barrier penetration the VolSurf model was able to predict the BBB profile for most of the drugs in the external prediction set. In Caco-2 and MDCK permeation experiments, VolSurf was used with success to establish statistical models and to predict the behaviour of new compounds. The method thus appears as a valuable new property filter in virtual screening and as a novel tool in optimizing the pharmacokinetic profile of pharmaceutically relevant compounds.

Natural history of clinically compensated hepatitis C virus-related graft cirrhosis after liver transplantation

The natural history of clinically compensated hepatitis C virus (HCV) cirrhosis after liver transplantation is unknown. This information is relevant to transplant centers to improve the management of these patients and decide the optimal timing for retransplantation. The aims of the study were (1) to describe the natural history of patients with HCV-cirrhosis transplants in a center with annual liver biopsies, and (2) to determine predictors for clinical decompensation, retransplantation, and mortality rates. A total of 49 patients with HCV-graft cirrhosis, 39 clinically compensated at histologic diagnosis of cirrhosis (post-liver transplantation cirrhosis) were included and followed up for 1 year (15 days-3.5 years). All patients tested were infected with genotype 1b. Predictive variables included histologic activity index (HAI) at post-liver transplantation cirrhosis, liver function tests, age, sex, and maintenance immunosuppression. Eighteen of 39 patients developed at least 1 episode of decompensation after a median of 7.8 months (4 days-2.6 years; 93% ascites). The cumulative probability of decompensation was 8%, 17%, and 42% at 1, 6, and 12 months, respectively. Graft and patient survival rates were 100%, 85%, and 71% and 100%, 92%, and 74% at 1, 6, and 12 months, respectively. Patient survival rates dropped significantly once decompensation developed (93%, 61%, and 41% at 1, 6, and 12 months, respectively). Variables associated with decompensation, retransplantation, and mortality rate included a high Child-Pugh score (>A), low levels of albumin at post-liver transplantation cirrhosis, and a short interval between liver transplantation and post-liver transplantation cirrhosis. The natural history of clinically compensated HCV-graft cirrhosis is shortened when compared with immunocompetent patients. If retransplantation is considered, it should be performed promptly once decompensation develops.

[Azathioprine and 5-ASA in the prevention of postoperative recurrence of Crohn's disease]

Recurrence of Crohn's disease (CD) lesions in the neo-ileum after apparently curative resection frequently occurs after surgery. The most appropriate prophylactic treatment has not been clearly defined. This study evaluated the efficacy of 5-ASA and azathioprine in decreasing postoperative recurrence and analysed the presence of variables associated with recurrence. Thirty-nine patients (mean age 32.8 years, range 18-61) with a history of ileal or ileocecal surgical resection were studied. They received 5-ASA (3 mg/day) or azathioprine (50 mg/day) immediately after the operation and for 2 years thereafter. Patients were followed clinically (Crohn's disease activity index) and serologically every 3 months and by imaging methods every 6 months. The latter included colonoscopy with ileoscopy and if not available, small bowel barium or ultrasonographic study. Laboratory tests included ESR, C-reactive protein, white blood cell and platelet count, fibrinogen and albumin. The end-point evaluated included clinical recurrence (CR), serological recurrence (SR: alteration of at least three of the above-mentioned variables) and morphologic recurrence (MR: endoscopic recurrence > 1 according to Rutgeerts score or radiological or ultrasonographic recurrence). Eighteen patients received azathioprine and 21 received 5-ASA. Thirty-four patients were evaluated. The cumulative proportion of patients with recurrence was 29% (CR), 35% (SR) and 50% (MR). Statistical analysis did not show significant differences between the two groups. Twenty-seven patients completed the 2-year study (11 in the azathioprine group and 16 in the 5-ASA group). Crude relapse rates were 37% (CR), 44% (SR) and 69% (MR) in the 5-ASA group and 36% (CR), 45% (SR) and 64% (MR) in the azathioprine group. No statistically significant differences were observed between groups. No variables associated with recurrence were detected. In conclusion, treatment does not prevent a high percentage of postsurgical recurrence. 5-ASA (3 g/day) and azathioprine (50 mg/day) showed similar efficacy in the prevention of recurrence.

GRid-INdependent descriptors (GRIND): a novel class of alignment-independent three-dimensional molecular descriptors

Traditional methods for performing 3D-QSAR rely upon an alignment step that is often time-consuming and can introduce user bias, the resultant model being dependent upon and sensitive to the alignment used. There are several methods which overcome this problem, but in general the necessary transformations prevent a simple interpretation of the resultant models in the original descriptor space (i.e. 3D molecular coordinates). Here we present a novel class of molecular descriptors which we have termed GRid-INdependent Descriptors (GRIND). They are derived in such a way as to be highly relevant for describing biological properties of compounds while being alignment-independent, chemically interpretable, and easy to compute. GRIND are obtained starting from a set of molecular interaction fields, computed by the program GRID or by other programs. The procedure for computing the descriptors involves a first step, in which the fields are simplified, and a second step, in which the results are encoded into alignment-independent variables using a particular type of autocorrelation transform. The molecular descriptors so obtained can be used to obtain graphical diagrams called "correlograms" and can be used in different chemometric analyses, such as principal component analysis or partial least-squares. An important feature of GRIND is that, with the use of appropriate software, the original descriptors (molecular interaction fields) can be regenerated from the autocorrelation transform and, thus, the results of the analysis represented graphically, together with the original molecular structures, in 3D plots. In this respect, the article introduces the program ALMOND, a software package developed in our group for the computation, analysis, and interpretation of GRIND. The use of the methodology is illustrated using some examples from the field of 3D-QSAR. Highly predictive and interpretable models are obtained showing the promising potential of the novel descriptors in drug design.

GRID/CPCA: a new computational tool to design selective ligands

We present a computational procedure aimed at understanding enzyme selectivity and guiding the design of drugs with respect to selectivity. It starts from a set of 3D structures of the target proteins characterized by the program GRID. In the multivariate description proposed, the variables are organized and scaled in a different way than previously published methodologies. Then, consensus principal component analysis (CPCA) is used to analyze the GRID descriptors, allowing the straightforward identification of possible modifications in the ligand to improve its selectivity toward a chosen target. As an important new feature the computational method is able to work with more than two target proteins and with several 3D structures for each protein. Additionally, the use of a 'cutout tool' allows to focus on the important regions around the active site. The method is validated for a total number of nine structures of the three homologous serine proteases thrombin, trypsin, and factor Xa. The regions identified by the method as being important for selectivity are in excellent agreement with available experimental data and inhibitor structure-activity relationships.

3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands

Many heterocyclic amines (HCA) present in cooked food exert a genotoxic activity when they are metabolised (N-oxidated) by the human cytochrome P450 1A2 (CYP1A2h). In order to rationalize the observed differences in activity of this enzyme on a series of 12 HCA, 3D-QSAR methods were applied on the basis of models of HCA-CYP1A2h complexes. The CYP1A2h enzyme model has been previously reported and was built by homology modeling based on cytochrome P450 BM3. The complexes were automatically generated applying the AUTODOCK software and refined using AMBER. A COMBINE analysis on the complexes identified the most important enzyme-ligand interactions that account for the differences in activity within the series. A GRID/GOLPE analysis was then performed on just the ligands, in the conformations and orientations found in the modeled complexes. The results from both methods were concordant and confirmed the advantages of incorporating structural information from series of ligand-receptor complexes into 3D-QSAR methodologies.

[Comparative analysis of viral load by bDNA HCV RNA-2.0 and amplicor HCV monitor in patients with hepatitis C infection]

BACKGROUND

Two standardized techniques, Quantiplex (bDNA-2.0) and Amplicor Monitor have been evaluated for the quantification of virus load of HCV with these objectives: a) determinate the relationship between virus load and genotype, and b) evaluate the virus load in serial serum samples and in patients with normal or slightly increased liver enzymes in an area with a high prevalence of genotype 1.

RESULTS

A significant correlation of 0.7 (p < 0.0001) in virus load has been observed by both methods, but the virus load is smaller by Monitor than by Quantiplex and does not depend on genotype. The relationship Monitor/Quantiplex is smaller in patients with non-1 genotype than in patients with genotype 1a (p = 0.01) and 1b (p = 0.005). Virus characteristics are similar in patients with normal or slightly increased enzymes than in patients with high enzymes. Virus load by both methods is not related to the age, sex, know duration of the infection, transmission manner of the infection neither to the histologic activity index.

CONCLUSION

The virus load not depends on genotype. The determination of virus load in a single serum sample adequately reflects the virus load are in several serum samples in patients with chronic HCV infection. The genotype and the virus load are similar in patients with normal enzymes than in patients with high enzymes.

Long-term results after combined modality treatment for non-metastatic osteosarcoma

Since the introduction of multimodality treatment, the prognosis of patients with high-grade non-metastatic osteosarcoma has significantly improved. A retrospective review was performed to assess the long-term results of this approach in a single centre setting, and to investigate the impact of potential clinical prognostic factors. Between 1985 and 1993, 35 patients with stage II-A and II-B osteosarcoma underwent preoperative chemotherapy (high-dose methotrexate), wide surgery, and adjuvant chemotherapy (cisplatin-doxorubicin/bleo-mycin-cyclophosphamide-dactinomycin) (modified T-10A protocol). There were 19 males and 16 females. Median patient age was 17 y (range 12-42). Primary tumour sites were the extremities (83%) and axial bones (17%). In spite of an unfavourable grade 3-4 histologic response rate to high-dose methotrexate of 12%, 31 (88%) patients were able to undergo limb-sparing surgery and 28 (80%) were rendered disease free after the planned therapy. Median follow-up was 8 y. The actuarial overall survival and disease-free survival rates were 64% and 49% at 5 y, and 59% and 49% at 10 y, respectively. Tumour size and primary site were significant prognostic factors for survival in univariate analyses. In conclusion, long-term survival after combined modality treatment can be achieved in more than 60% of patients with localised osteosarcoma, including non-appendicular lesions. Limb-sparing surgery is a realistic goal for most cases. The prognostic value of tumour necrosis and the efficacy of neoadjuvant chemotherapy should be interpreted according to individual high-dose methotrexate scheduling.

Comparative analysis of quantification of viral load in patients infected with hepatitis C virus: quantiplex HCV RNA assay and amplicor monitor assay

OBJECTIVE

two standardized techniques, Quantiplex HCV RNA 2.0 (bDNA) and Amplicor Monitor, were evaluated for the quantification of hepatitis C virus (HCV) load. Our objectives were: 1) to determine the relationship between viral load and genotype, and 2) to evaluate viral load in serial serum samples and in patients with normal or slightly elevated liver enzyme values in an area with a high prevalence of genotype 1.

RESULTS

the viral loads detected with the two methods correlated significantly (r = 0.7, p < 0.0001), but viral load was smaller with the Monitor than with the Quantiplex assay, and was independent of genotype. The Monitor/Quantiplex ratio was lower in patients with a non-1 genotype than in patients with genotype 1b. Virological characteristics were similar in patients with normal or slightly elevated enzyme levels and in patients with elevated enzyme values. Neither method showed a relationship between viral load and age, sex, duration of the infection, mode of transmission, or histological activity index.

CONCLUSION

viral load was not dependent on genotype. Measurement of viral load in a single serum sample adequately reflected the viral load measured in several serum samples from patients with chronic HCV infection. Patients with normal liver enzyme levels are not good candidates, in virological terms, for treatment with interferon.

ESHAP is an active regimen for relapsing Hodgkin's disease

BACKGROUND

Refractory or relapsing Hodgkin's disease is associated with a poor prognosis. There is no widely accepted salvage chemotherapy regimen for these patients. However, the addition of high-dose chemotherapy followed by autologous hematopoietic transplantation (AHT) has proven of benefit to them. A prospective clinical trial was carried out to evaluate the efficacy and toxicity of ESHAP (etoposide, methylprednisolone, high-dose cytarabine, and cisplatin).

PATIENTS AND METHODS

Twenty-two patients with refractory (5) or relapsing Hodgkin's disease (17) were entered and scheduled to receive three courses of ESHAP. Patients suitable for AHT were then given high-dose chemotherapy with CBV (cyclophosphamide, carmustine, and etoposide) plus AHT, whereas responding, non-AHT-suitable patients completed six ESHAP courses.

RESULTS

Nine patients achieved complete responses and seven partial responses (overall response rate 73%) with ESHAP. Grade 3-4 myelotoxicity was seen in 13 patients (59%). Nine patients received CBV plus AHT. At a median follow-up time of 50 months (range 6-96), seven patients (32%) are alive and disease-free. Three patients died of toxic effects of ESHAP (1) or CBV (2). Actuarial overall survival and disease-free survival were 35% and 27% at three years.

CONCLUSIONS

ESHAP is an active regimen for relapsing Hodgkin's disease, with myelosuppression as its dose-limiting toxicity. An increased risk of treatment-related mortality when it is combined with high-dose chemotherapy can not be ruled out.

[The effect of iron depletion on the response to interferon treatment in patients with chronic hepatitis C. Pilot study]

It has been reported that increase in serum ferritin levels and/or in hepatic iron content is associated with a poor response to interferon treatment in patients with chronic hepatitis C (CH-C).

AIM

To determinate whether iron depletion by phlebotomy (PB) increases the response to interferon therapy in chronic hepatitis C.

PATIENTS AND METHODS

We have evaluated 12 patients with CH-C (genotype 1b = 11, 1a = 1), increased ALT levels, positive serum VHC-RNA and increased serum ferritin levels (> 220 ng/ml), including 8 previously non responders to interferon therapy and 4 naive subjects. Phlebotomies were performed weekly (mean number per patient: 6, range: 5-12) until serum ferritin levels were < 100 ng/ml, followed by interferon treatment (3MU thrice weekly for 3-12 months depending on the response).

RESULTS

Multiple regression analysis showed that serum ferritin levels were not related to serum ALT levels (p = 0.18) or viral load (p = 0.06). Serum ALT levels decreased significantly post-PB (58 U/l, range: 35-141 U/l) as compared to pretreatment levels (164 U/l, range: 51-216 U/l, p < 0.006) and normalized in two subjects. HCV-RNA was positive in one of the latter and negative in the other. Eleven of the twelve patients did not respond to interferon after three months of therapy (increased serum ALT levels in 10 subjects and positive HCV RNA in 11). One additional patient, who had not been treated previously with interferon and had low pretreatment viral load, had a sustained response after 12 months of interferon therapy. Viral load did not decreased either with PB or following interferon treatment. By contrast, serum ferritin levels did not increase with interferon treatment or during the 6 month follow-up period.

CONCLUSIONS

Decreasing serum ferritin levels by phlebotomies does not increase HCV erradication rate after interferon treatment. Sustained response to interferon therapy is an infrequent event and is more dependent on viral factors (viral load and genotype).

Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design

A comparative binding energy (COMBINE) analysis (Ortiz et al. J. Med. Chem. 1995, 38, 2681-2691) has been performed on a training set of 33 HIV-1 protease inhibitors, and the resulting regression models have been validated using an additional external set of 16 inhibitors. This data set was originally reported by Holloway et al. (J. Med. Chem. 1995, 38, 305-317), who showed the usefulness of molecular mechanics interaction energies for predicting the activity of novel HIV-1 protease inhibitors within the framework of the MM2X force field and linear regression techniques. We first used the AMBER force field on the same set of three-dimensional structures to check up on any possible force-field dependencies. In agreement with the previous findings, the calculated raw ligand-receptor interaction energies were highly correlated with the inhibitory activities (r2 = 0.81), and the linear regression model relating both magnitudes had an acceptable predictive ability both in internal validation tests (q2 = 0.79, SDEPcv = 0.61) and when applied to the external set of 16 different inhibitors (SDEPex = 1.08). When the interaction energies were further analyzed using the COMBINE formalism, the resulting PLS model showed improved fitting properties (r2 = 0.89) and provided better estimations for the activity of the compounds in the external data set (SDEPex = 0.83). Computation of the electrostatic part of the ligand-receptor interactions by numerically solving the Poisson-Boltzmann equation did not improve the quality of the linear regression model. On the contrary, incorporation of the solvent-screened residue-based electrostatic interactions and two additional descriptors representing the electrostatic energy contributions to the partial desolvation of both the ligands and the receptor resulted in a COMBINE model that achieved a remarkable predictive ability, as assessed by both internal (q2 = 0.73, SDEPcv = 0.69) and external validation tests (SDEPex = 0.59). Finally, when all the inhibitors studied were merged into a single expanded set, a new model was obtained that explained 91% of the variance in biological activity (r2 = 0.91), with very high predictive ability (q2 = 0.81, SDEPcv = 0.66). In addition, the COMBINE analysis provided valuable information about the relative importance of the contributions to the activity of individual residues that can be fruitfully used to design better inhibitors. All in all, COMBINE analysis is validated as a powerful methodology for predicting binding affinities and pharmacological activities of congeneric ligands that bind to a common receptor.

[Free bowel perforation as the onset and as a complication in the evolution of crohn's disease]

Free bowel perforation is a relatively infrequent complication of Crohn's disease. It may present during the evolution of the disease or, occasionally, in the onset of the same and may involve the small intestine or colon. We herein present 4 cases, three of ileal localization and one of colonic localization. In one of the 3 former cases and the latter case perforation took place prior to diagnosis of the disease. Review of the literature was performed with respect to the frequency, pathogenesis and characteristics of this complication and the importance of determined diagnostic techniques such as echography and CAT in addition to the most adequate treatment are commented upon.

Long-term follow-up and prognostic factors in Ewing's sarcoma. A multivariate analysis of 116 patients from a single institution

The records of 116 patients from a single center (1970-1993) with newly diagnosed Ewing's sarcoma or primitive neuroectodermal tumor were reviewed retrospectively. The aim of this study was to ascertain the impact of pretreatment variables on disease-free survival. Median age was 14 years (range 1-34). Twenty patients presented with metastatic disease. Treatment consisted of systemic multiagent chemotherapy plus local irradiation (39%), wide resection (22%), or both (35%). Median potential follow-up was 10.7 years (range 2-26). Three patients developed second malignancies (1 breast carcinoma, 2 acute myeloid leukemias). Median time to relapse was 24 months (range 3-143). The actuarial disease-free survival was 37.4% at 5 years, 33.3% at 10 years and 27.8% at 15 years. Neoadjuvant chemotherapy and a therapy-induced tumor necrosis > or = 90% were associated with a better outcome. Patients undergoing surgical resection had a superior disease-free survival than those treated without surgery (45 vs. 18% at 10 years, p = 0.0009). Multiple regression analysis showed that raised serum lactate dehydrogenase levels (p < 0.001), hypoalbuminemia (p = 0.001) and distant metastases at diagnosis (p = 0.03) were independent adverse prognostic factors. In conclusion, one third of patients with Ewing's sarcoma become long-term survivors with combined modality treatment. Late relapses and second neoplasms are of concern. Prognostic factors should be considered in the selection of therapy, and the value of serum albumin warrants confirmatory studies.

A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis

Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

Simulation of alternative binding modes in a structure-based QSAR study of HIV-1 protease inhibitors

We have used a published set of inhibitors of HIV-1 protease to build a COMBINE-type structure-based QSAR model with good predictive ability (r2 = 0.90, q2 = 0.69). Since the compounds in the training series exhibit most of their structural variability on one-half of the pseudosymmetrical binding cavity and only one binding orientation was explored for each molecule, the model describes mainly the effect of the structural changes on interactions involving only one-half of the binding cavity (pockets S1' and S2'). Thus, the model cannot be expected to give accurate predictions for new compounds exhibiting structural variation in both halves. The model does in fact show a tendency to underpredict slightly the biological activity of the molecules in the external test set. In an attempt to improve the quality of the model, both possible orientations of the ligands are now considered so that structural variation takes place in all binding pockets. One possibility would have been to build an additional set of complexes with the inhibitors docked in a reversed orientation. The alternative we have explored, however, consists of manipulating the data matrix describing the interaction energies so that each row is duplicated and the order of the variables in the duplicated rows is swapped between subunits. This simple approach has produced a new model that is similar in quality to the original model (r2 = 0.89, q2 = 0.64) but lacks the tendency to underpredict the activity of the compounds in the external set. Moreover, since equivalent residues are assigned equivalent weights, the model is insensitive to ligand orientation and is easier to interpret.

Pretreatment prognostic factors for survival in small-cell lung cancer: a new prognostic index and validation of three known prognostic indices on 341 patients

AIMS

a) To identify which pretreatment clinical or blood parameters were predictive of patients survival in small-cell lung cancer (SCLC) in a retrospective analysis. b) To validate three known prognostic indices: Royal Marsden Model (index 1), London Group (index 2) and Manchester Score (index 3).

PATIENTS AND METHODS

From 1981 to 1993, 341 SCLC patients were treated with chemotherapy with or without surgery or radiotherapy. Univariate and multiple regression analyses of survival were performed and the feasibility of these models was explored, index 1: Karnofsky index, albumin, sodium and alkaline phosphatase; index 2: ECOG performance status (PS), albumin and alanine transaminase; and index 3; lactate dehydrogenase (LDH), disease extent, sodium, Karnofsky index, alkaline phosphatase and bicarbonate.

RESULTS

Significant prognostic factors for survival after univariate and multiple regression analysis were: disease extent, PS, creatine kinase, neutrophilia, LDH, hypoalbuminemia, hyperglycemia and bicarbonate. A new prognostic index was performed that included LDH, hypoalbuminemia, neutrophilia, disease extent and PS. It defined three prognostic groups (PG). Median survival and two-year survival for these PG were 12.3, 8 and 3.4 months and 16.5%, 2.3% and 0%, respectively. The following PG were identified after application of the three models proposed: Index 1 identified two PG with 0% and 16.6% two-year survival (P < 0.001); index 2 detected three PG with 0%, 5% and 15.7% two-year survival (P < 0.001) and index 3 detected three PG with 0%, 2.5% and 16.2% two-year survivals, respectively (P < 0.001).

CONCLUSION

A new prognostic index is proposed allowing identification of three different PG. The feasibility of three known prognostic models was validated and demonstrated. Variables other than disease extent or PS (albumin or LDH) should be taken into account in designing future clinical trials.

Smart region definition: a new way to improve the predictive ability and interpretability of three-dimensional quantitative structure-activity relationships

This report describes a new methodology aimed at grouping 3D-QSAR interaction energy descriptors into regions of neighbor variables bearing the same chemical and statistical information. These regions represent the structural variability of the series better than individual descriptor variables and can advantageously replace them in the chemometric analysis. The algorithm used to generate such regions is described, together with their application for improving the quality of GOLPE variable selection. The method is illustrated on a series of 47 glucose analogues, inhibitors of glycogen phosphorylase b, and is shown to improve both the predictive ability and the interpretability of the 3D-QSAR models obtained, comparing favorably with other methods previously described.

[The effect of controlled release of DOPA and carbidopa on clinical response and plasma pharmacokinetics of DOPA in parkinsonian patients]

This is a multicentric double blind comparison of the effects of standard and slow release levodopa + carbidopa formulations in patients with Parkinson's disease. Sixty four patients with simple fluctuations were included and 43 finished the study. The study had three phases: a) optimal dose findings phase with standard levodopa + carbidopa; b) open label, cross over study with the two formulations, and c) double blind, parallel investigation. The following results were obtained. There was not a difference in the severity of disability according to UPDRS, part 3, scores though the subjective impressions of patients were in favor of standard formulations. The Sustained release levodopa + carbidopa produced significant improvement of dystonia in off period, pain due to akinesia in off and the number of hours in off and the quality and latency of sleep. In addition there was a tendency in favor of slow release compounds for early morning akinesia, global effect and impression of the examining physician. Low protein diet improved the kinetics of levodopa and the clinical response with both formulations. The clinical usefulness of standard and slow release levodopa + carbidopa formulation should be weighted according to individual problems of patients with Parkinson's disease.