Step-by-step design of proteins for small molecule interaction: a review on recent milestones

Protein design is the field of synthetic biology that aims at developing de-novo custom made proteins and peptides for specific applications. Despite exploring an ambitious goal, recent computational advances in both hardware and software technologies have paved the way to high-throughput screening and detailed design of novel folds and improved functionalities. Modern advances in the field of protein design for small molecule targeting are described in this review, organized in a step-by-step fashion: from the conception of a new or upgraded active binding site, to scaffold design, sequence optimization and experimental expression of the custom protein. In each step, contemporary examples are described, and state-of-the art software is briefly explored.publishe

Macular hole formation, progression, and surgical repair: case series of serial optical coherence tomography and time lapse morphing video study

<p>Abstract</p> <p>Background</p> <p>To use a new medium to dynamically visualize serial optical coherence tomography (OCT) scans in order to illustrate and elucidate the pathogenesis of idiopathic macular hole formation, progression, and surgical closure.</p> <p>Case Presentations</p> <p>Two patients at the onset of symptoms with early stage macular holes and one patient following repair were followed with serial OCTs. Images centered at the fovea and at the same orientation were digitally exported and morphed into an Audiovisual Interleaving (avi) movie format. Morphing videos from serial OCTs allowed the OCTs to be viewed dynamically. The videos supported anterior-posterior vitreofoveal traction as the initial event in macular hole formation. Progression of the macular hole occurred with increased cystic thickening of the fovea without evidence of further vitreofoveal traction. During cyst formation, the macular hole enlarged as the edges of the hole became elevated from the retinal pigment epithelium (RPE) with an increase in subretinal fluid. Surgical repair of a macular hole revealed initial closure of the macular hole with subsequent reabsorption of the sub-retinal fluid and restoration of the foveal contour.</p> <p>Conclusions</p> <p>Morphing videos from serial OCTs are a useful tool and helped illustrate and support anterior-posterior vitreofoveal traction with subsequent retinal hydration as the pathogenesis of idiopathic macular holes.</p

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Anti-VEGF treatment of macular edema associated with retinal vein occlusion: patterns of use and effectiveness in clinical practice (ECHO study report 2)

J Michael Jumper,1 Pravin U Dugel,2,3 Sanford Chen,4 Kevin J Blinder,5 John G Walt6 On behalf of the ECHO Study Group 1West Coast Retina Medical Group, San Francisco, CA, USA; 2Retinal Consultants of Arizona, Phoenix, AZ, USA; 3USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; 4Orange County Retina, Santa Ana, CA, USA; 5The Retina Institute, St Louis, MO, USA; 6Allergan plc, Irvine, CA, USA Purpose: To evaluate the efficacy, safety, and injection frequency of vascular endothelial growth factor (VEGF) antagonists in the treatment of macular edema secondary to retinal vein occlusion (RVO) in clinical practice.Patients and methods: A multicenter retrospective study of the medical records of 165 patients (95 branch RVO, 70 central RVO) treated with at least three anti-VEGF injections in the study eye was conducted. Available data collected for at least 6 months after the first injection included Snellen best-corrected visual acuity (BCVA), central retinal thickness (CRT) by time-domain optical coherence tomography (TD-OCT) or spectral-domain optical coherence tomography (SD-OCT), anti-VEGF injections, other treatments/procedures for RVO, and adverse events.Results: At baseline prior to anti-VEGF treatment, mean BCVA was 20/80 Snellen equivalent and mean CRT was 499 &micro;m. Mean number of anti-VEGF injections received was 7.1 during the first year, 5.4 during the second year, and 5.9 during the third year; 51.3% (842/1,641) of injections were ranibizumab, 44.1% (724/1,641) were bevacizumab, and 4.6% (75/1,641) were aflibercept. One in five patients received concomitant focal laser treatment. The percentage of patients achieving both BCVA of 20/40 or better and CRT &le;250 &micro;m on TD-OCT or &le;300 &micro;m on SD-OCT at the same visit (primary endpoint) was 26.1% (30/115) after the first anti-VEGF injection and ranged from 20.0% (7/35) to 36.7% (11/30) after the first 16 injections. After each anti-VEGF injection from the 1st to the 16th, &lt;60% of patients achieved 20/40 or better BCVA and &le;70% of patients achieved CRT &le;250 &micro;m on TD-OCT or &le;300 &micro;m on SD-OCT. The most common treatment-related adverse event was blurry or cloudy vision.Conclusion: In this real-world study, a mean of five to seven anti-VEGF injections was administered yearly, and the response to anti-VEGF therapy was suboptimal in many patients. Anti-VEGF therapy was well tolerated. Keywords: aflibercept, bevacizumab, branch retinal vein occlusion, central retinal vein occlusion, ranibizumab, visual acuity&nbsp

Anti-VEGF treatment of diabetic macular edema in clinical practice: effectiveness and patterns of use (ECHO Study Report 1)

Kevin J Blinder,1 Pravin U Dugel,2,3 Sanford Chen,4 J Michael Jumper,5 John G Walt,6 David A Hollander,6 Lanita C Scott6 On behalf of the ECHO Study Group 1The Retina Institute, St Louis, MO, 2Retinal Consultants of Arizona, Phoenix, AZ, 3USC Roski Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, 4Orange County Retina, Santa Ana, 5West Coast Retina Medical Group, San Francisco, 6Allergan plc, Irvine, CA, USA Purpose: To evaluate the efficacy, safety, and injection frequency of vascular endothelial growth factor (VEGF) inhibitors as used in clinical practice for the treatment of diabetic macular edema.Methods: Multicenter (10 sites), retrospective chart review in patients (n=156) who received &ge;3 anti-VEGF injections. Data collected for &ge;6&nbsp;months after the first injection included Snellen best-corrected visual acuity (BCVA) and central retinal thickness (CRT) by time-domain or spectral-domain optical coherence tomography (TD-OCT or SD-OCT).Results: Mean number of anti-VEGF injections (627 bevacizumab, 594 ranibizumab, 1 aflibercept) was 5.8 (year 1), 5.0 (year 2), and 3.4 (year 3). Percentage of patients with BCVA of 20/40 or better and CRT &le;250&nbsp;&micro;m on TD-OCT or &le;300&nbsp;&micro;m on SD-OCT at the same visit (primary endpoint) ranged from 16.4% to 38.9% after the first 10 injections; 51.9%&ndash;62.3% achieved &ge;20/40 BCVA and 26.2%&ndash;48.0% met CRT criteria. Therapy was well tolerated with 19 treatment-related adverse events (all ocular) reported.Conclusion: Anti-VEGF injections were administered less frequently and were less effective than those in the ranibizumab registration trials. After each of the first 9 injections, &lt;25% of patients achieved both BCVA of 20/40 or better and a dry macula. A substantial proportion of patients are suboptimal responders to anti-VEGF therapy; these patients may be candidates for other therapies, including intravitreal corticosteroid and laser therapy. Keywords: bevacizumab, diabetic retinopathy, drug administration schedule, ranibizumab, vascular endothelial growth factor, visual acuit

Spectral domain optical coherence tomography findings in patients with acute syphilitic posterior placoid chorioretinopathy

PURPOSE: To describe the appearance of acute syphilitic posterior placoid chorioretinitis, a rare ocular manifestation of syphilis, on spectral domain optical coherence tomography (SD OCT) both before and after treatment. METHODS: Ophthalmic examination and imaging studies of 30 eyes of 19 confirmed cases were analyzed both at the time of presentation and at each follow-up visit. Patients with SD OCT and fluorescein angiography at the time of presentation, and at least three documented follow-up visits after initiation of therapy, were included in the study. Standard treatment of neurosyphilis was given to each patient, including 4 million units of penicillin G administered intravenously every 4 hours for 14 days. RESULTS: Fundus examination and imaging studies were consistent with previous reports and confirmed the diagnosis of acute syphilitic posterior placoid chorioretinitis. In 13 eyes (43.3%), baseline SD OCT scans were performed within 1 to 2 days of presentation and revealed a small amount of subretinal fluid, disruption of the inner segment/outer segment junction, and hyperreflective thickening of the retinal pigment epithelium (RPE). All 30 eyes were again scanned between Days 7 and 9 after presentation and revealed loss of the inner segment/outer segment and OS/RPE bands, and irregular hyperreflectivity of the RPE with prominent nodular elevations but without subretinal fluid. Early disruption of the external limiting membrane and punctate choroidal hyperreflectivity were seen in 1 of the 30 eyes (3.3%) and 14 of the 30 eyes (46.6%), respectively. Vision improved and the outer retinal abnormalities normalized in 28 of the 30 eyes (93.3%) after the treatment of neurosyphilis. The external limiting membrane, inner segment/outer segment band, and/or linear outer segment/RPE junction remained substantially abnormal despite treatment in 2 eyes left with 20/200 vision. CONCLUSION: Patients with acute syphilitic posterior placoid chorioretinitis show characteristic outer retinal abnormalities on SD OCT imaging, including disruption of the inner segment/outer segment band, nodular thickening of the RPE with loss of the linear outer segment/RPE junction, and, in some cases, loss of the external limiting membrane, accumulation of subretinal fluid, and punctate hyperreflectivity in the choroid. Vision improved and these abnormalities reversed after treatment of neurosyphilis in most of the patients. Persistently, poor vision despite treatment was associated with long-term loss or disruption of outer retinal anatomy on SD OCT. Copyright © by Ophthalmic Communications Society, Inc

Spectral domain optical coherence tomography findings in patients with acute syphilitic posterior placoid chorioretinopathy.

PURPOSE: To describe the appearance of acute syphilitic posterior placoid chorioretinitis, a rare ocular manifestation of syphilis, on spectral domain optical coherence tomography (SD OCT) both before and after treatment. METHODS: Ophthalmic examination and imaging studies of 30 eyes of 19 confirmed cases were analyzed both at the time of presentation and at each follow-up visit. Patients with SD OCT and fluorescein angiography at the time of presentation, and at least three documented follow-up visits after initiation of therapy, were included in the study. Standard treatment of neurosyphilis was given to each patient, including 4 million units of penicillin G administered intravenously every 4 hours for 14 days. RESULTS: Fundus examination and imaging studies were consistent with previous reports and confirmed the diagnosis of acute syphilitic posterior placoid chorioretinitis. In 13 eyes (43.3%), baseline SD OCT scans were performed within 1 to 2 days of presentation and revealed a small amount of subretinal fluid, disruption of the inner segment/outer segment junction, and hyperreflective thickening of the retinal pigment epithelium (RPE). All 30 eyes were again scanned between Days 7 and 9 after presentation and revealed loss of the inner segment/outer segment and OS/RPE bands, and irregular hyperreflectivity of the RPE with prominent nodular elevations but without subretinal fluid. Early disruption of the external limiting membrane and punctate choroidal hyperreflectivity were seen in 1 of the 30 eyes (3.3%) and 14 of the 30 eyes (46.6%), respectively. Vision improved and the outer retinal abnormalities normalized in 28 of the 30 eyes (93.3%) after the treatment of neurosyphilis. The external limiting membrane, inner segment/outer segment band, and/or linear outer segment/RPE junction remained substantially abnormal despite treatment in 2 eyes left with 20/200 vision. CONCLUSION: Patients with acute syphilitic posterior placoid chorioretinitis show characteristic outer retinal abnormalities on SD OCT imaging, including disruption of the inner segment/outer segment band, nodular thickening of the RPE with loss of the linear outer segment/RPE junction, and, in some cases, loss of the external limiting membrane, accumulation of subretinal fluid, and punctate hyperreflectivity in the choroid. Vision improved and these abnormalities reversed after treatment of neurosyphilis in most of the patients. Persistently, poor vision despite treatment was associated with long-term loss or disruption of outer retinal anatomy on SD OCT