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.

Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors

The effects of data pretreatment, data scaling, and variable selection on three-dimensional quantitative structure-activity relationships derived by comparative molecular field analysis (CoMFA) using the GRID energy function were studied in detail for a set of inhibitors of the human synovial fluid phospholipase A2 (HSF-PLA2). The quality of the models was evaluated for predictive power and ability to map the receptor binding site by (a) comparison of predicted and experimental activities using cross-validation and external validation sets and (b) comparison of the regions selected in space in the CoMFA models with a crystal structure of a HSF-PLA2-inhibitor complex, with optimized comparative binding energy analysis (COMBINE) models (Ortiz et al., 1995) and with structure-activity relationships derived previously for different sets of compounds. It is found that (1) data scaling and dielectric modeling strongly influence CoMFA results. Unscaled data and a uniform dielectric constant of 4 are well suited to GRID-CoMFA studies for the present compound set. (2) The GOLPE and Q2-GRS variable selection methods select variables in roughly the same regions in Cartesian space, but they produce different models in chemometric space and differ in their sensitivity to data scaling and pretreatment and their tendency to overfitting. (3) CoMFA models are consistent with COMBINE models in that they identify approximately the same intermolecular interactions as relevant for activity. Our study provides support for the qualitative receptor-mapping properties of CoMFA models and for the validity of variable selection when applied with care and also provides guidelines for how to evaluate the quality of CoMFA models.

GRID/GOLPE 3D quantitative structure-activity relationship study on a set of benzamides and naphthamides, with affinity for the dopamine D3 receptor subtype

In the search for drugs against schizophrenia and depression without extrapyramidal side effects, compounds that selectively antagonize the dopamine D3 receptor subtype are thought to be a solution. In order to create a model with which the D3 activity can be predicted and that can generate new ideas for future synthesis, we performed a comparative molecular field analysis (CoMFA). In our model 30 ligands were described quantitatively in the GRID program, and the model was optimized by selecting only the most informative variables in the GOLPE program. We found the predictive ability of the model to increase significantly when the number of variables was reduced from 25110 to 784. A Q2 of 0.65 was obtained with the final model, confirming the predictive ability of the model. By studying the PLS coefficients in informative 3D contour plots, ideas for the synthesis of new compounds can be generated.

A systems approach to asthma care

This two-year asthma intervention focuses on provider education emphasizing early diagnosis of asthma, early use of oral steroids, proper use of inhalation devices, objective monitoring of patient status, and use of daily preventive treatment. Patient education is an integral part of treatment. This approach supports the primary care physician as the provider and coordinator of care by supplying monitoring and treatment devices, books, diaries, home care services, and allergy consultation. It also manifests a systems approach to asthma care in its reliance on a nurse case manager who oversees patient and family support network.

Randomised comparison of ceftazidime and imipenem as initial monotherapy for febrile episodes in neutropenic cancer patients

With the availability of new, broad-spectrum antibiotics, initial therapy with a single agent has become an alternative to classic combinations in the management of febrile, neutropenic cancer patients. The aims of this study were to compare the efficacy of ceftazidime and imipenem as empirical monotherapy of febrile episodes in neutropenic patients, and to examine the frequency with which second-line antibiotics (amikacin, vancomycin, or both) were required. A prospective clinical trial was carried out in a single centre. Eligible patients with solid tumours or lymphoma were randomised to receive monotherapy with ceftazidime or imipenem. In the event of no response, amikacin and/or vancomycin were added in 48-72 h intervals (sequentially, or according to clinical or microbiological data). Efficacy was evaluable for 111 assessable episodes. Median neutrophil count at entry was 100 cells/microliters and median duration of neutropenia was 4 days. Febrile episodes were classified as microbiologically (34%) or clinically documented (42%), and fever of unknown origin (24%). Gram-negative infections (57%) predominated over gram-positive isolates (30%). The overall success rate with monotherapy (69% versus 70%), or with modification (20% versus 23%) were equivalent for ceftazidime and imipenem (P = 0.75). The mortality in this series was 5%. Single-agent therapy with either ceftazidime or imipenem is effective for the empirical treatment of febrile episodes in neutropenic patients with solid tumours. Early addition of amikacin and/or vancomycin resolves most failures of the first step.

Intravitreal ganciclovir for cytomegalovirus retinitis in patients with AIDS

OBJECTIVE

To assess the evolution of cytomegalovirus (CMV) retinitis and evaluate the possible complications associated with the use of intravitreal injections to treat this disease.

DESIGN

A nonrandomized, retrospective study with case series was performed. The study took place over 34 months.

SETTING

The study included patients with AIDS who developed CMV retinitis, and who were treated in the hospital, as outpatients, or both.

PATIENTS

Twelve patients with AIDS and CMV retinitis diagnosed between June 1990 through April 1993 were included in the study. MAIN PATIENT PARAMETERS AND OUTCOME MEASURES: For each patient, the following data were recorded: age, risk factors, other systemic findings, dates of AIDS and CMV retinitis diagnoses, stage of AIDS, extent of the retinitis, CD4 lymphocyte count at the time of diagnosis of retinitis, visual acuity, clinical evolution of the ocular infection, therapy, complications caused by the treatment, development on nonocular CMV, and the use of zidovudine or didanosine during the study period.

RESULTS

Vision improved or remained stable in nine patients and worsened in three. Two patients developed optic neuritis. The retinitis progressed to the other eye in only one of the eight patients who had unilateral involvement. The rate of relapse with maintenance therapy was 8.3% (n = 1) within the first 8 weeks. Treatment was well tolerated. There was no evidence of toxicity after a total of 226 intravitreal ganciclovir injections. All patients were able to tolerate zidovudine or didanosine concomitantly with intravitreal ganciclovir.

CONCLUSIONS

Intravitreal ganciclovir appears to be an effective alternate to systemic ganciclovir in patients with severe neutropenia and in patients who choose to continue receiving systemic zidovudine or didanosine. Early treatment and long-term maintenance therapy is essential for preserving sight.

Retrospective study of the correlation between the DNA repair protein alkyltransferase and survival of brain tumor patients treated with carmustine

We tested the hypothesis that the level of the DNA repair protein O6-alkylguanine-DNA alkyltransferase in brain tumors was correlated with resistance to carmustine (BCNU) chemotherapy. Alkyltransferase levels in individual cells in sections from 167 primary brain tumors treated with BCNU were quantitated with an immunofluorescence assay using monoclonal antibodies against human alkyltransferase. Patients with high levels of alkyltransferase had shorter time to treatment failure (P = 0.05) and death (P = 0.004) and a death rate 1.7 times greater than patients with low alkyltransferase levels. Furthermore, the size of the subpopulation of cells with high levels of alkyltransferase was correlated directly with drug resistance. For all tumors the variables most closely correlated with survival, in order of importance, were age, tumor grade, and alkyltransferase levels. For glioblastoma multiforme, survival was more strongly correlated with alkyltransferase levels than with age. These results should encourage prospective studies to evaluate alkyltransferase levels as a method, for identifying brain tumor patients with the best likelihood of response to BCNU chemotherapy.

Extragonadal nongestational choriocarcinoma involving the lung: a report of three cases

Primary choriocarcinoma of the lung is an extremely rare tumour, with about 20 cases reported in the literature. The case records of 3 female patients with nongestational, extragonadal choriocarcinoma apparently arising in the lung are presented to illustrate its clinical spectrum, the utility of serum beta human chorionic gonadotropin, and responsiveness to chemotherapy. Most plausible origins of these malignancies and differential diagnosis are briefly discussed.

A novel strategy for improving ligand selectivity in receptor-based drug design

A major desirable characteristic of many drugs is their ability to interact specifically with only one variety of the target receptor among many others. It is remarkable that, even when accurate three dimensional structures for the target biomolecules are available, there is no well-established methodology to describe their differences and use them for the design of selectively-interacting compounds. This work presents a novel method that uses multivariate GRID descriptors and principal component analysis (PCA) with the aim of revealing the most relevant structural and physicochemical differences between biomacromolecules related to receptor selectivity. The methodology is described through an example involving the study of bacterial (Escherichia coli) and recombinant human varieties of the dihydrofolate reductase (EC 1.5.1.3, DHFR) enzyme. This analysis easily unveils the most important regions on these biomolecules which should be taken into consideration for the design of selectively interacting compounds.

Synthesis, structure, and pharmacological evaluation of the stereoisomers of furnidipine

The synthesis and pharmacological activities of the four stereoisomers of methyl tetrahydrofuran-2-ylmethyl 2,6-dimethyl-4-(2'-nitrophenyl)-1,4-dihydropyridine-3,5- dicarboxylate(furnidipine) are reported. The four isomers were synthesized by a modified Hantzsch synthesis by reaction of (-)- or (+)-tetrahydrofuran-2-ylmethyl 3-aminocrotonate and methyl 2-[(2'-nitrophenyl)methylene]acetoacetate or, alternatively, by reaction of (-)- or (+)-tetrahydrofuran-2-ylmethyl 2-[(2'-nitrophenyl)methylene]acetoacetate and methyl 3-aminocrotonate. The 1:1 diastereomeric mixtures thus obtained were separated by chromatography, using poly(D-phenylglycine) as the chiral stationary phase. The enantiomeric purity of the stereoisomers was determined by a high-performance liquid chromatography-chiral stationary phase technique (HPLC-CSP). Attempts to obtain crystals of a single stereoisomer failed in different solvents, while methanol crystallization of the product obtained from (+/-)-tetrahydrofuran-2-ylmethyl 2-[(2'-nitrophenyl)methylene]acetoacetate and methyl 3-aminocrotonate yielded good-quality crystals of the most insoluble racemate which proved to be a mixture of the (SS)/(RR) enantiomers by X-ray crystallography. Conformational analysis of the stereoisomers, assuming rotation of the aryl substituent and ester groups, shows small energy differences (about 4 kcal.mol-1) between the most and the least favorable conformations. Binding studies were performed using [3H]isradipine as a reference ligand. The results showed stereospecificity of the furnidipine isomers in brain, ileum, and cardiac tissues, the (SS)- and (SR)-isomers clearly being more potent than their (RR)- and (RS)-enantiomers. The (SS)- and (SR)-isomers were also more selective on cerebral tissue when compared with ileal and cardiac preparations.

Extragonadal germ cell tumors: prognostic factors and long-term follow-up

The records of 23 patients (22 male and 1 female, median age 28 years) with extragonadal germ cell tumors (EGCT) treated between 1974 and 1993 were reviewed retrospectively to investigate long-term survival and prognostic factors. Treatment consisted of cisplatin-based chemotherapy plus local irradiation or surgery. There were 7 seminomas, 5 poorly differentiated carcinomas (PDC) with elevated biomarkers, and 11 nonseminomatous germ cell tumors (NSGCT). The primary sites were retroperitoneum (10 cases), mediastinum (5 cases), pineal gland (4 cases) and other (4 cases). Two partial and 14 complete responses (69.6% overall) were achieved with primary therapy. After a median follow-up of 63 months, 10 (43.5%) patients live disease-free and 5-year survival is 55%. Seminomas showed an excellent outcome. Retroperitoneal NSGCT behaved like testicular neoplasms. Between nonseminoma patients, PDC histology and mediastinal primary were associated with the worst prognoses. EGCT patients should be treated and reported separately according to histology and primary site.

Cholinergic modulation of immunoglobulin secretion from avian plasma cells: the role of calcium

The existence of a functional connection between the nervous and immune systems has long been argued. To determine if such a link exists in the secretory immune system, we have examined the avian lacrimal gland (Harderian gland) which contains large numbers of plasma cells. We have shown that these plasma cells bind an antibody to muscarinic acetylcholine receptor and that carbachol, an acetylcholine agonist, increases the secretion rate of IgG by these cells above a constitutive baseline level. This neurotransmitter-dependent increase of immunoglobulin secretion requires an influx of Ca2+, whereas the constitutive baseline secretion is apparently less dependent on such a flux. Furthermore, the Ca2+ flux appears to be mediated by voltage-dependent calcium channels. These data support the hypothesis that plasma cells can respond to neurotransmitters and, in the case of acetylcholine, increase immunoglobulin secretion.