Combinatorial assembly and design of enzymes.

The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.

Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions.

Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard-Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain conformations for Ile, Leu, Phe, Thr, Trp, Tyr and Val. This result shows that there are no alternative, sterically allowed side chain conformations of core residues. Analysis of the same set of protein cores using the Rosetta software suite revealed that the hard-sphere model and Rosetta perform equally well on Ile, Leu, Phe, Thr and Val; the hard-sphere model performs better on Trp and Tyr and Rosetta performs better on Ser. We conclude that the high prediction accuracy in protein cores obtained by protein modeling software and our simplified hard-sphere approach reflects the high density of protein cores and dominance of steric repulsion.

Predictors of duloxetine response in patients with oxaliplatin-induced painful chemotherapy-induced peripheral neuropathy (CIPN): a secondary analysis of randomised controlled trial - CALGB/alliance 170601.

Duloxetine is an effective treatment for oxaliplatin-induced painful chemotherapy-induced peripheral neuropathy (CIPN). However, predictors of duloxetine response have not been adequately explored. The objective of this secondary and exploratory analysis was to identify predictors of duloxetine response in patients with painful oxaliplatin-induced CIPN. Patients (N = 106) with oxaliplatin-induced painful CIPN were randomised to receive duloxetine or placebo. Eligible patients had chronic CIPN pain and an average neuropathic pain score ≥4/10. Duloxetine/placebo dose was 30 mg/day for 7 days, then 60 mg/day for 4 weeks. The Brief Pain Inventory-Short Form and the EORTC QLQ-C30 were used to assess pain and quality of life, respectively. Univariate and multiple logistic regression analyses were performed to identify demographic, physiologic and psychological predictors of duloxetine response. Higher baseline emotional functioning predicted duloxetine response (≥30% reduction in pain; OR 4.036; 95% CI 0.999-16.308; p = 0.050). Based on the results from a multiple logistic regression using patient data from both the duloxetine and placebo treatment arms, duloxetine-treated patients with high emotional functioning are more likely to experience pain reduction (p = 0.026). In patients with painful, oxaliplatin-induced CIPN, emotional functioning may also predict duloxetine response. ClinicalTrials.gov, Identifier NCT00489411.

L-carnitine supplementation for the treatment of fatigue and depressed mood in cancer patients with carnitine deficiency: a preliminary analysis.

Nutritional factors are among the postulated causes of fatigue, a highly prevalent symptom in the cancer population, with serious impact on patients' quality of life. Deficiency of the micronutrient carnitine may play a role by reducing energy production through fatty acid oxidation. We present preliminary data of an open-label, dose-finding study to determine safety and maximally tolerated dose (MTD) of 1 week of L-carnitine supplementation in cancer patients with fatigue and carnitine deficiency. Patients who met inclusion/exclusion criteria underwent carnitine level determination. Eighty-three percent of these patients (15/18) had carnitine deficiency. Preliminary data analysis of 13 patients showed that total carnitine increased from 30.0 +/- 6.9 to 41.0 +/- 12.1 (mean +/- SD) after 1 week of supplementation (P = 0.01), and free carnitine increased from 24.3 +/- 6.1 to 33.8 +/- 9.8 (P = 0.004). Outcome measures were fatigue (BFI score), depression (CES-D), sleep disruption (ESS), and performance status (Karnofsky). Median (min, max) BFI score at baseline was 73 (46, 82) versus 50 (3, 82) after 1-week supplementation (P = 0.009). CES-D score at baseline was 29 (16, 42) and 22 (8, 32) after 1 week (P = 0.028). ESS at baseline was 46.5 (0, 69) and 30.4 (0, 72) after 1 week (P = 0.015). Karnofsky score did not change significantly (P = 0.38). We are currently conducting a randomized, double-blind, placebo-controlled study to rigorously assess the role of L-carnitine for the treatment of fatigue and depression in cancer patients.

A new era in the pharmacologic management of type 2 diabetes.

This article offers an overview of the variety of pharmacologic treatments available to Type 2 diabetes patients. This surge of options has unfolded over the past 7-8 years, and has made the "one treatment fits all" approach an antiquated concept. A basic understanding of the complex physiology underlying Type 2 diabetes is addressed and is a prerequisite to understanding the mechanisms of the various medications. By grouping the oral agents for diabetes into physiologic categories, it is hoped that the reader will attain a clear image of these medications, both singularly and in combination.

Involving family members in cancer care: focus group considerations of patients and oncological providers.

Family members are an integral part of a patient's cancer care from the moment the diagnosis is delivered to the conclusion of treatment. Family members bring with them a range of emotional reactions, interpersonal dynamics and expectations for the care the patient receives. This study is part of a multi-institutional project to continue to improve the process of cancer care. In this study, 19 focus groups (11 patient and 8 provider) were conducted concerning issues related to doctor-patient communication in eight cancer centers in the United States. The content of the conversations was analyzed and thematic categories emerged that highlight the various strengths and difficulties associated with family involvement. The focus groups' comments support the need for explicit conversations between professional caregivers, patients and their loved ones, in order to negotiate the expectations and needs of each team member. Implications for clinical practice and strategies for working with family members are offered.

A pilot study of interpersonal psychotherapy by telephone with cancer patients and their partners.

A single-arm pilot study explored the feasibility of adapting in Interpersonal Psychotherapy (IPT) by telephone to reduce psychological distress and to enhance coping during cancer treatment. Therapy focuses on role transitions, interpersonal conflicts, and grief precipitated by cancer. Breast cancer patients receiving high-dose chemotherapy received weekly sessions with a psychologist throughout chemotherapy and for 1 month afterwards. Patients could invite one 'partner' to receive individual telephone IPT. Psychosocial functioning was assessed using standardized measures at study entry, after chemotherapy, and following telephone IPT. Accrual and participation supplied evidence of feasibility: 14 patients and 10 partners were recruited, 82.5% of those eligible. Patients had a mean of 16 sessions; partners had a mean of 11. Participants rated their satisfaction with the program between 'good' and 'excellent'. A test of the efficacy of telephone IPT requires a larger, randomized trial. In order to standardize the intervention, a treatment manual was developed. This study indicated the importance of outreach to family members as well as to cancer patients, intensive patient education about oncology treatment and the medical care setting, and psychosocial services that continue after cancer treatment has been completed.

Is quality of life predictive of the survival of patients with advanced nonsmall cell lung carcinoma?

BACKGROUND: Several studies have recently reported on the importance of quality of life (QOL) in predicting the survival of patients with lung carcinoma. To confirm these reports, the relationship between survival and QOL, as measured by the European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire and Duke-UNC Social Support Scale, was examined within a group of 206 patients with advanced nonsmall cell lung carcinoma treated in a randomized clinical trial conducted by the Cancer and Leukemia Group B (CALGB 8931). METHODS: Patients completed the EORTC instrument and the Duke-UNC Social Support Scale at baseline in the clinic. The Cox proportional hazards model was used to determine the incremental contribution QOL provided in predicting survival beyond the effect of known clinical prognostic variables. RESULTS: Clinical factors that were jointly predictive of poorer survival included low performance status, nonadenocarcinoma histology, presence of dyspnea, weight loss greater than 5%, albumin level less than 3.5 mg/dL, and adrenal metastases. Univariate analyses showed that patient-reported EORTC subscales describing increased pain, appetite loss, fatigue, lung carcinoma symptoms, poorer overall QOL, and poorer physical functioning predicted significantly poorer survival. Multivariate analyses showed that, after adjustment for clinical factors, overall QOL was not a significant predictor of survival. Rather, the only EORTC subscale of prognostic importance was the pain subscale, in which a 40-point increase was associated with a 27% increase in the hazard rate. CONCLUSIONS: This study did not confirm the prognostic importance of overall QOL. Rather, after adjustment for significant clinical factors, a patient-provided pain report had the greatest prognostic importance.

A longitudinal study of quality of life in advanced non-small cell lung cancer: Cancer and Leukemia Group B (CALGB) 8931.

A quality of life (QOL) endpoint supplemented standard clinical endpoints of survival, tumor response, and toxicity in a double-blind study conducted by the Cancer and Leukemia Group B (CALGB) where 291 patients with advanced non-small cell lung cancer (NSCLC) were randomly assigned to receive cisplatin/vinblastine with either hydrazine sulfate (HS) or placebo. The difficulties associated with the analysis of the longitudinal QOL data, and the contributions that the QOL endpoint made to the understanding of treatment differences, will be the focus of this paper.

Supportive telephone intervention for patients receiving chemotherapy. A pilot study.

Psychosocial interventions have been shown to improve quality of life (QOL) for many cancer patients. A pilot study was conducted to assess the feasibility of a psychoeducational intervention for cancer patients receiving chemotherapy. Eight patients receiving chemotherapy for colorectal carcinoma participated. The intervention is based on a modification of Interpersonal Therapy. It consisted of four sessions, administered biweekly, using a manual format, by a psychiatric nurse clinician over the telephone. The participants also completed a set of QOL measures by telephone to assess tolerance of the planned assessment. The patients received assistance with treatment-related side effects, reported improved ability to communicate with their physician, and gained an understanding of the stresses they discussed. The patients felt satisfied with the emotional support and medical information provided. A randomized trial is planned to test the intervention for patients participating in a cooperative trial sponsored by the National Cancer Institute.

Free-riding and the prisoner's dilemma: problems in funding economic analyses of phase III cancer clinical trials.

PURPOSE: Both economic and clinical data on new agents are important to policy-makers who approve pharmaceuticals for widespread use. Randomized clinical trials have been used to evaluate both clinical results and total medical costs associated with new agents. With new expensive pharmaceutical agents, early assessments of economic benefit have taken on greater importance to physicians and patients. Who should provide financial support to these integrated economic and clinical analyses in clinical trials? Here we describe issues that hinder funding of economic analyses and propose potential support mechanisms. RESULTS: The Cancer and Leukemia Group B (CALGB), a large, national cooperative group of academic and community hospitals in the United States, designed a non-small-cell lung cancer (NSCLC) treatment trial to compare two widely used supportive care regimens that varied 20-fold in cost. One important objective of this trial was to compare the cost-effectiveness of the two regimens. While funding for the clinical trial was supported by grants from the National Cancer Institute and the pharmaceutical companies involved in the trial, no specific funding agency was willing and/or able to provide financial support for the economic analyses. After 2 years of planning, the clinical trial was retracted when the funding for the economic analyses could not be secured. The prisoner's dilemma, individual reluctance to support a common social good, explains the lack of funding. CONCLUSION: Economic theory predicts difficulties in evaluating cost-effectiveness of new pharmaceuticals and reluctance to support economic analyses of clinical trials. Economic analyses will require new sources of funds that will not take scarce resources from clinical trials groups. Options for funding include a new federal agency, coordinated work by existing agencies, or academic centers for economic analysis.

Cisplatin, vinblastine, and hydrazine sulfate in advanced, non-small-cell lung cancer: a randomized placebo-controlled, double-blind phase III study of the Cancer and Leukemia Group B.

PURPOSE: To assess the chemotherapy regimen of cisplatin, vinblastine, and hydrazine sulfate administered to patients with non-small-cell lung cancer (NSCLC) in a randomized, placebo-controlled double-blind phase III study. PATIENTS AND METHODS: Between July 25, 1989 and February 1, 1991, 291 patients with stage IIIB or IV NSCLC and performance status 0 or 1 were randomized to receive cisplatin 100 mg/m2 intravenously (IV) every 28 days, vinblastine 5 mg/m2 IV per week times five, then every 2 weeks; and either hydrazine sulfate 60 mg three times per day orally or placebo. The concurrent use of corticosteroids, medroxyprogesterone, or other appetite stimulants was not permitted. Treatment groups were comparable for known prognostic variables. The primary end point of this study was survival; however, the influence of hydrazine sulfate on nutritional status, performance status, and quality of life was also assessed. RESULTS: Analysis of 266 eligible patients showed a median survival duration of 7.78 months for the hydrazine sulfate-treated group compared with 7.70 months for the placebo-treated group (P = .65, log-rank). Objective response rates were similar for the two groups, with 4% complete responses, 20% partial responses, and 2% regressions in those treated with hydrazine sulfate; 3% complete responses, 23% partial responses, and 2% regressions in those who received placebo. The major toxicity was severe or life-threatening neutropenia, which occurred in 65% of hydrazine sulfate patients and 63% of placebo patients. There were no differences noted between the two groups in degree of anorexia, weight gain or loss, or overall nutritional status. Sensory and motor neuropathy occurred significantly more often in patients treated with hydrazine sulfate. Quality of life was significantly worse in patients who received hydrazine sulfate. CONCLUSION: This study suggests no benefit from the addition of hydrazine sulfate to an effective cytotoxic regimen.

Antiemetic-induced akathisia in cancer patients receiving chemotherapy.

A structured, prospective telephone interview was used to assess the prevalence of akathisia in 24 cancer patients receiving metoclopramide or prochlorperazine during or after chemotherapy. Half of the patients reported subjective motor restlessness, and 75% stated that they would not have informed staff. This report suggests that akathisia is frequently unrecognized in chemotherapy patients receiving metoclopramide and prochlorperazine.

The European Organization for Research and Treatment of Cancer QLQ-C30: a quality-of-life instrument for use in international clinical trials in oncology.

BACKGROUND: In 1986, the European Organization for Research and Treatment of Cancer (EORTC) initiated a research program to develop an integrated, modular approach for evaluating the quality of life of patients participating in international clinical trials. PURPOSE: We report here the results of an international field study of the practicality, reliability, and validity of the EORTC QLQ-C30, the current core questionnaire. The QLQ-C30 incorporates nine multi-item scales: five functional scales (physical, role, cognitive, emotional, and social); three symptom scales (fatigue, pain, and nausea and vomiting); and a global health and quality-of-life scale. Several single-item symptom measures are also included. METHODS: The questionnaire was administered before treatment and once during treatment to 305 patients with nonresectable lung cancer from centers in 13 countries. Clinical variables assessed included disease stage, weight loss, performance status, and treatment toxicity. RESULTS: The average time required to complete the questionnaire was approximately 11 minutes, and most patients required no assistance. The data supported the hypothesized scale structure of the questionnaire with the exception of role functioning (work and household activities), which was also the only multi-item scale that failed to meet the minimal standards for reliability (Cronbach's alpha coefficient > or = .70) either before or during treatment. Validity was shown by three findings. First, while all interscale correlations were statistically significant, the correlation was moderate, indicating that the scales were assessing distinct components of the quality-of-life construct. Second, most of the functional and symptom measures discriminated clearly between patients differing in clinical status as defined by the Eastern Cooperative Oncology Group performance status scale, weight loss, and treatment toxicity. Third, there were statistically significant changes, in the expected direction, in physical and role functioning, global quality of life, fatigue, and nausea and vomiting, for patients whose performance status had improved or worsened during treatment. The reliability and validity of the questionnaire were highly consistent across the three language-cultural groups studied: patients from English-speaking countries, Northern Europe, and Southern Europe. CONCLUSIONS: These results support the EORTC QLQ-C30 as a reliable and valid measure of the quality of life of cancer patients in multicultural clinical research settings. Work is ongoing to examine the performance of the questionnaire among more heterogenous patient samples and in phase II and phase III clinical trials.

Semiautomated reminder system for improving syphilis management.

This project utilized an automated record system, COSTAR, to assess and improve the quality of care in managing syphilis in a health maintenance organization. A scoring tool was developed to assess care. There were four experimental periods, each lasting one year. The periods were Baseline (no intervention), Education (publication of guidelines and an educational session), Reminder (deficiencies in care brought to the attention of providers in time to permit correction), and Post-reminder (no intervention). Scores for overall management of syphilis rose from 70.4 to 90.5% during the Reminder period and did not deteriorate significantly in the Post-reminder period. Scores in the Education period were not significantly higher than baseline. The cost of the system was $195 per year. An inexpensive reminder system was effective in bringing about a significant improvement in quality of care for syphilis, and the effect persisted for at least a year after the system was discontinued.