Improving virtual screening of G protein-coupled receptors via ligand-directed modeling

G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state

Induction chemotherapy followed by chemoradiotherapy versus chemoradiotherapy alone as neoadjuvant treatment for locally recurrent rectal cancer: study protocol of a multicentre, open-label, parallel-arms, randomized controlled study (PelvEx II)

Background A resection with clear margins (R0 resection) is the most important prognostic factor in patients with locally recurrent rectal cancer (LRRC). However, this is achieved in only 60 per cent of patients. The aim of this study is to investigate whether the addition of induction chemotherapy to neoadjuvant chemo(re)irradiation improves the R0 resection rate in LRRC. Methods This multicentre, international, open-label, phase III, parallel-arms study will enrol 364 patients with resectable LRRC after previous partial or total mesorectal resection without synchronous distant metastases or recent chemo- and/or radiotherapy treatment. Patients will be randomized to receive either induction chemotherapy (three 3-week cycles of CAPOX (capecitabine, oxaliplatin), four 2-week cycles of FOLFOX (5-fluorouracil, leucovorin, oxaliplatin) or FOLFORI (5-fluorouracil, leucovorin, irinotecan)) followed by neoadjuvant chemoradiotherapy and surgery (experimental arm) or neoadjuvant chemoradiotherapy and surgery alone (control arm). Tumours will be restaged using MRI and, in the experimental arm, a further cycle of CAPOX or two cycles of FOLFOX/FOLFIRI will be administered before chemoradiotherapy in case of stable or responsive disease. The radiotherapy dose will be 25 × 2.0 Gy or 28 × 1.8 Gy in radiotherapy-naive patients, and 15 × 2.0 Gy in previously irradiated patients. The concomitant chemotherapy agent will be capecitabine administered twice daily at a dose of 825 mg/m2 on radiotherapy days. The primary endpoint of the study is the R0 resection rate. Secondary endpoints are long-term oncological outcomes, radiological and pathological response, toxicity, postoperative complications, costs, and quality of life. Discussion This trial protocol describes the PelvEx II study. PelvEx II, designed as a multicentre, open-label, phase III, parallel-arms study, is the first randomized study to compare induction chemotherapy followed by neoadjuvant chemo(re)irradiation and surgery with neoadjuvant chemo(re)irradiation and surgery alone in patients with locally recurrent rectal cancer, with the aim of improving the number of R0 resections

Avaliação das respostas fisiológicas de bezerros zebuínos puros e cruzados nascidos em clima subtropical Evaluation of physiological responses of straightbred and crossbred Zebu calves born in a subtropical environment

Estudou-se a influência de fatores climáticos sobre as respostas fisiológicas de bezerros, puros e cruzados, filhos de vacas da raça Nelore ou de alta mestiçagem de Nelore acasaladas com touros das raças Aberdeen Angus (AN), Simental (SN), Canchim (CN) e Nelore (NI e NR). Os bezerros AN, SN, CN e NI foram mantidos em sistema rotacionado intensivo, enquanto o grupo NR foi mantido em sistema extensivo. Os bezerros foram observados de forma direta desde o nascimento até a primeira mamada, medindo-se a latência para a primeira mamada (LM). Aproximadamente 24 horas após o parto, coletaram-se amostras de sangue do bezerro para as dosagens de proteína total (PT), glicose (Gli), triiodotironina (T3), tiroxina (T4), relação T4:T3, cortisol (Cort) e imunoglobulina G (IgGb), além das medidas de temperatura retal do bezerro (TR) e dos pesos de vacas e bezerros. Para análise dos efeitos de clima, foram tomadas no dia do nascimento as medidas de temperatura do ar (Temp), umidade do ar (UR) e precipitação (PRE). Os parâmetros fisiológicos foram estudados pelo método dos quadrados mínimos com modelos que incluíram os efeitos de ano e mês de nascimento, grupo e sexo do bezerro, categoria da vaca e hora do parto e das interações ano &times; grupo e ano &times; mês de nascimento, além das covariáveis peso do bezerro, PRE, Temp, UR e LM. Temp mostrou efeito significativo para as concentrações de T3, T4, T4:T3 e de Cort. Quanto maior Temp, menores as concentrações de T3 e de Cort e maiores as de T4 e de T4:T3. LM influenciou os níveis de Cort, PT e IgGb, de modo que, quanto maior LM, maior a concentração de Cort e menor as de IgGb e PT. Também houve efeito significativo de grupo do bezerro sobre PT, que foi maior nos bezerros NR que nos bezerros NI.<br>The influence of environmental parameters on the physiological responses of purebred and crossbred Nellore calves born in a subtropical region was studied. All calves were born from high grade Nellore cows sired by Aberdeen Angus (AN), Simmental (SN), Canchim (CN) and Nellore (NI) bulls. These calves were raised under intensive management and another group of Nellore calves (NR) was raised under extensive management, similar to the typical brazilian system for beef production. Calves were observed from birth until the end of the first suckling, and the variable first suckling latency (LM) was estimated. Aapproximately 24 hours after birth, blood samples were collected from each calf to measure the plasma concentrations of total protein (PT), glucose (Gli), triiodothyronin (T3), thyroxin (T4), T3:T4 ratio, cortisol (Cort) and immunoglobulin-G (IgGb). At the same time, the calves' rectal temperature was taken and the cows and the calves were weighed. Climatic data of temperature (Temp), relative humidity (UR) and rain precipitation (PRE) in the birth day were also recorded. Physiological parameters were analyzed by least squares method using a model that included the effects of year and month of calving, group of calf, sex of calf, cow category, calving time, year &times; group and year &times; month of birth interactions and the covariables calf's weight, PRE, Temp, UR and LM. The effect of Temp was significant for the concentrations of T3, T4, T4:T3 and Cort. The concentrations of T3 and Cort decreased and the levels of T4 and T4:T3 ratio increased as Temp increased. Similarly, the concentration of Cort increased and the concentrations of IgGb and PT decreased as LM increased. PT level was significantly higher in NR calves than in NI ones