Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes.

Over the past five decades, tremendous effort has been devoted to computational methods for predicting properties of ligands-i.e., molecules that bind macromolecular targets. Such methods, which are critical to rational drug design, fall into two categories: physics-based methods, which directly model ligand interactions with the target given the target's three-dimensional (3D) structure, and ligand-based methods, which predict ligand properties given experimental measurements for similar ligands. Here, we present a rigorous statistical framework to combine these two sources of information. We develop a method to predict a ligand's pose-the 3D structure of the ligand bound to its target-that leverages a widely available source of information: a list of other ligands that are known to bind the same target but for which no 3D structure is available. This combination of physics-based and ligand-based modeling improves pose prediction accuracy across all major families of drug targets. Using the same framework, we develop a method for virtual screening of drug candidates, which outperforms standard physics-based and ligand-based virtual screening methods. Our results suggest broad opportunities to improve prediction of various ligand properties by combining diverse sources of information through customized machine-learning approaches.

Quality of Life Associated with Nausea and Vomiting from Anthracycline-Based Chemotherapy: A Pooled Data Analysis from Three Prospective Trials.

BACKGROUND: There is limited work on the impact of chemotherapy-induced nausea and vomiting (CINV) on quality of life (QoL) in adriamycin-cyclophosphamide (AC)-treated patients with breast cancer. The objectives of the study were the following: (a) to confirm if symptoms of CINV led to lower QoL during AC; (b) to evaluate the pattern of changes in patients' QoL during multiple cycles of AC; and (c) to assess if the QoL in an earlier cycle affected the QoL in subsequent cycles of AC. MATERIALS AND METHODS: This is a secondary pooled data analysis that included 303 Chinese patients with breast cancer who received 1,177 cycles of adjuvant AC in three prospective antiemetic studies. QoL data were based on Functional Living Index-emesis (FLIE) scored over three to four AC cycles. CINV symptoms assessed included "no significant nausea" (NSN), "significant nausea" (SN), "no vomiting" (NoV), "vomiting" (V), and complete response (CR). RESULTS: Across all AC cycles, the mean scores for the FLIE nausea domain for patients who experienced NSN versus SN were 10.92 versus 53.92, respectively (p < .0001), with lower scores indicating better QoL; the mean scores for the FLIE vomiting domain for patients who experienced NoV versus V were 1.44 versus 19.11, respectively (p < .0001), with similar results across subsequent cycles. Analysis of the effect of the QoL in cycle 1 on the QoL of subsequent cycles revealed the following: for the nausea domain, among patients who had cycle 1 FLIE scores ≥ versus < the mean, the corresponding scores in cycle 2 were 6.87 versus 36.71 (p < .0001); whereas those for cycle 3 were 7.07 versus 36.87 (p < .0001); and those for cycle 4 were 5.92 versus 21.48 (p < .0001). Similar findings were observed for the vomiting domain. Netupitant + palonosetron- or aprepitant/olanzapine-based antiemetics had significantly better QoL outcomes. CONCLUSION: CINV had a significant impact on the QoL of patients with breast cancer treated with AC over multiple cycles. IMPLICATIONS FOR PRACTICE: In this post-hoc analysis of three prospective studies on chemotherapy-induced nausea and vomiting (CINV), quality of life (QoL) using contemporary antiemetic regimens in Chinese breast cancer patients receiving doxorubicin-cyclophosphamide (AC) was evaluated. During the first and subsequent AC cycles, QoL was significantly better for patients who did not experience vomiting or significant nausea. QoL in an earlier cycle affected the QoL in subsequent AC cycles. Furthermore, recent regimens involving olanzapine/aprepitant or netupitant-palonosetron were associated with a positive impact in QoL. Antiemetic guideline-consistent practice and higher clinician awareness of the impact of CINV on QoL can further mitigate the negative effects of CINV on QoL.

Longitudinal change of quality of life in the first five years of survival among disease-free Chinese breast cancer survivors.

PURPOSE: This study aimed to investigate changes of QoL during the first 5 years of survival among disease-free Chinese breast cancer survivors. METHODS: A prospective cohort study enrolled 1462 Chinese women with early-stage breast cancer, and longitudinally visited those patients at four time-points, namely baseline (T0), 18- (T1), 36- (T2), and 60-month (T3) after diagnosis. This study included 992 patients who were disease-free during the first 5 years of survival and who had completed QoL assessments at all four time-points. RESULTS: The score of global health status/QoL improved gradually (T1, T2, T3 > T0; P < 0.001 for overall comparisons). Social functioning score significantly improved when compared to that of T0 (T1, T2, T3 > T0; P < 0.001 for overall comparisons). In contrast, cognitive functioning score decreased (T0 > T1, T2, T3; P < 0.001 for overall comparisons). Scores of physical functioning, role functioning and emotional functioning showed a fluctuated picture, with the highest score achieved at T1. In symptoms profile, most of them scored lowest at T1 (best QoL). Multivariate analysis showed that several characteristics significantly correlated to changes in QoL from T0 to T3. For instance, patients with higher education had better recovery of physical functioning, role functioning, and social functioning. CONCLUSION: During the first 5 years of survival, patients' global health status/QoL improved over time, social functioning consistently improved, but cognitive functioning steadily deteriorated. Most of functioning domains and symptoms improved at 18-month follow-up, but such improvements were not maintained and even deteriorated at 36- and 60-month post-diagnosis. This study suggested that some interventions should be investigated during such period.

State of the Art Antiemetic Therapy for Cancer Patients.

Nausea and vomiting are common in cancer patients. The most common cause of nausea and vomiting is the administration of cytotoxic chemotherapy. Apart from chemotherapy-induced nausea and vomiting (CINV), biological agents may also cause these symptoms. In this review, discussion will be focused on management of nausea and vomiting due to antineoplastic therapies. The cornerstone of effective management of nausea and vomiting secondary to these antineoplastic drugs is the prevention with the use of appropriate guideline-directed combination antiemetic regimen. Type 3 serotonin receptor antagonists (5HT3RAs), neurokinin-1 receptor antagonists (NK1RAs), and dexamethasone are the backbone antiemetic drugs. In recent years, newer drugs and preparations have been introduced for clinical use and include second-generation 5HT3RA, palonosetron; granisetron transdermal patch; the recently introduced NK1RA rolapitant; and the novel oral combined drug NEPA (netupitant plus palonosetron); and last but not least, the atypical antipsychotic olanzapine.

Risk Factors Associated with Chemotherapy-Induced Nausea and Vomiting Among Women with Breast Cancer Receiving Highly Emetogenic Chemotherapy: Individual Patient-Based Analysis of Three Prospective Antiemetic Trials.

Purpose: Although risk factors related to chemotherapy-induced nausea and vomiting (CINV) have been identified in previous studies, only a few studies have evaluated the risk factors associated with contemporary antiemetic prophylaxis, including olanzapine/aprepitant- or NEPA-containing regimens. This study aimed to identify the risk factors associated with CINV development in Chinese breast cancer patients receiving doxorubicin and cyclophosphamide chemotherapy. Methods: Data from 304 patients enrolled in 3 previously reported prospective antiemetic studies were included. Multivariate logistic regression models were used to predict risk factors associated with CINV occurrence. Additionally, the likelihood of treatment failure in relation to the number of risk factors in individual patients was evaluated. Results: Multivariate analysis of the entire study group revealed that obesity status (defined as body mass index/= 25.0 kg/m2) and the use of olanzapine/aprepitant- or NEPA-containing anti-emetic regimens were associated with a high likelihood, while a history of motion sickness was associated with a lower likelihood, complete response (CR), and "no nausea" in the overall phase. A history of vomiting during pregnancy was also associated with a lower likelihood of an overall CR. Patients with an increasing number of risk factors had a higher likelihood of treatment failure and shorter time to first vomiting. Those who did not achieve CR and "no nausea" in the first cycle were less likely to achieve these parameters in the subsequent cycle of chemotherapy. Conclusion: The present study confirmed previously reported risk factors for CINV in Chinese breast cancer patients receiving doxorubicin and cyclophosphamide. Further optimization of CINV control is required for patients with identifiable risk factors; olanzapine/aprepitant- or NEPA- containing prophylaxis are the preferred contemporary anti-emetics regimens for Chinese breast cancer patients undergoing doxorubicin and cyclophosphamide chemotherapy.

Dynamic Changes of Post-Radiotherapy Plasma Epstein-Barr Virus DNA in a Randomized Trial of Adjuvant Chemotherapy Versus Observation in Nasopharyngeal Cancer.

PURPOSE: To study the dynamic changes in plasma Epstein-Barr virus (pEBV) DNA after radiotherapy in nasopharyngeal cancer (NPC). EXPERIMENTAL DESIGN: We conducted a randomized controlled trial of adjuvant chemotherapy versus observation in patients with NPC who had detectable pEBV DNA at 6 weeks post-radiotherapy. Randomized patients had a second pEBV DNA checked at 6 months post-randomization. The primary endpoint was progression-free survival (PFS). RESULTS: We prospectively enrolled 789 patients. Baseline post-radiotherapy pEBV DNA was undetectable in 573 (72.6%) patients, and detectable in 216 (27.4%) patients, of whom 104 (13.2%) patients were eligible for randomization to adjuvant chemotherapy (n = 52) versus observation (n = 52). The first post-radiotherapy pEBV DNA had a sensitivity of 0.48, specificity of 0.81, area under receiver-operator characteristics curve (AUC) of 0.65, false positive (FP) rate of 13.8%, and false negative (FN) rate of 14.4% for disease progression. The second post-radiotherapy pEBV DNA had improved sensitivity of 0.81, specificity of 0.75, AUC of 0.78, FP rate of 14.3%, and FN rate of 8.1%. Patients with complete clearance of post-radiotherapy pEBV DNA (51%) had survival superior to that of patients without post-radiotherapy pEBV DNA clearance (5-year PFS, 85.5% vs. 23.3%; HR, 9.6; P < 0.0001), comparable with patients with initially undetectable post-radiotherapy pEBV DNA (5-year PFS, 77.1%), irrespective of adjuvant chemotherapy or observation. CONCLUSIONS: Patients with NPC with detectable post-radiotherapy pEBV DNA who experienced subsequent pEBV DNA clearance had superior survival comparable with patients with initially undetectable post-radiotherapy pEBV DNA. Post-radiotherapy pEBV DNA clearance may serve as an early surrogate endpoint for long-term survival in NPC.

Dataset on chemotherapy-induced nausea and vomiting (CINV) and quality of life (QOL) during multiple chemotherapy cycles among a Chinese breast cancer patient population who were randomized to antiemetic regimens with or without olanzapine.

Chemotherapy-induced nausea and vomiting (CINV) are highly distressing symptoms for cancer patients undergoing cytotoxic chemotherapy. This dataset was obtained from a homogenous group of Chinese breast cancer patients who were uniformly planned to receive a highly emetogenic (neo)adjuvant chemotherapy regimen, consisting of doxorubicin and cyclophosphamide (commonly known as AC). Patients were being randomized to one of the two antiemetic regimens: aprepitant, ondansetron and dexamethasone with (the Olanzapine arm) or without olanzapine (the Standard arm). Patients underwent self-reported diaries and questionnaires to record their nausea and vomiting symptoms, use of rescue medication as well as their quality of life (QOL). The primary and secondary endpoints have focused on efficacy analysis during the first cycle of AC chemotherapy; the results have been reported in The Breast [1]. In this Data in Brief article, we provide outcome of the analysis of data collected during multiple cycles of chemotherapy. The data reported here include the proportion of patients with "Complete Response", "Complete Protection" and "Total Control" of emesis in the acute (0-24 h), delayed (24-120 h) and overall periods (0-120 h), as well as QOL data during all the 4 cycles of AC.

Transient left ventricular apical ballooning syndrome (takotsubo cardiomyopathy) as a complication of permanent pacemaker implantation.

BACKGROUND: Takotsubo cardiomyopathy is a rare and newly described clinical entity characterized by transient left ventricular apical ballooning and left ventricular apical dyskinesis in the absence of angiographic evidence of significant coronary vessel disease found predominantly in post-menopausal women. It was first documented in the USA in 2004, and it has previously been described only in Japanese and Caucasian patients. CASE REPORT: A 77-year-old Native Hawaiian woman was admitted to the hospital for severe bradycardia. To the best of our knowledge, this is the first time that normal ventricular function has been documented by echocardiography just prior to the development of the syndrome of transient left ventricular apical ballooning. METHODS: Retrospective review of the reported patient's medical record, cardiac angiography and ventriculography, echocardiography, and ECGs. DISCUSSION: The patient reported manifested all of the diagnostic criteria for transient left ventricular apical ballooning syndrome proposed by the Mayo Clinic. The finding of normal cardiac morphology and contractility by echocardiography two days prior to diagnosis shows that this syndrome develops rapidly. The case reported here is the first time that transient left ventricular apical ballooning syndrome has been documented in a Native Hawaiian patient in a tropical location, suggesting that transient left ventricular apical ballooning likely occurs across all ethnic and geographical lines.