Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors

Hepatitis C virus (HCV) infects millions of people worldwide, causing chronic liver disease that can lead to cirrhosis, hepatocellular carcinoma, and liver transplant. In the last several years, the advent of direct-acting antivirals, including NS3/4A protease inhibitors (PIs), has remarkably improved treatment outcomes of HCV-infected patients. However, selection of resistance-associated substitutions and polymorphisms among genotypes can lead to drug resistance and in some cases treatment failure. A proactive strategy to combat resistance is to constrain PIs within evolutionarily conserved regions in the protease active site. Designing PIs using the substrate envelope is a rational strategy to decrease the susceptibility to resistance by using the constraints of substrate recognition. We successfully designed two series of HCV NS3/4A PIs to leverage unexploited areas in the substrate envelope to improve potency, specifically against resistance-associated substitutions at D168. Our design strategy achieved better resistance profiles over both the FDA-approved NS3/4A PI grazoprevir and the parent compound against the clinically relevant D168A substitution. Crystallographic structural analysis and inhibition assays confirmed that optimally filling the substrate envelope is critical to improve inhibitor potency while avoiding resistance. Specifically, inhibitors that enhanced hydrophobic packing in the S4 pocket and avoided an energetically frustrated pocket performed the best. Thus, the HCV substrate envelope proved to be a powerful tool to design robust PIs, offering a strategy that can be translated to other targets for rational design of inhibitors with improved potency and resistance profiles.IMPORTANCE Despite significant progress, hepatitis C virus (HCV) continues to be a major health problem with millions of people infected worldwide and thousands dying annually due to resulting complications. Recent antiviral combinations can achieve \u3e 95% cure, but late diagnosis, low access to treatment, and treatment failure due to drug resistance continue to be roadblocks against eradication of the virus. We report the rational design of two series of HCV NS3/4A protease inhibitors with improved resistance profiles by exploiting evolutionarily constrained regions of the active site using the substrate envelope model. Optimally filling the S4 pocket is critical to avoid resistance and improve potency. Our results provide drug design strategies to avoid resistance that are applicable to other quickly evolving viral drug targets

Synthesis and Kinetic Analysis of HCV NS3/4a Protease Inhibitors

Hepatitis C virus (HCV) is the leading cause of chronic liver disease in the world. To make more effective antiviral therapies, companies started to develop direct acting antiviral drugs that could target specific components of the virus. One target is the NS3/4a protease and while inhibitors (PIs) have been developed, but are susceptible to drug-resistant mutations. The goal of the project was to develop new PIs based on the drug MK-5172 and test inhibition on both wild type and mutant proteases. Three inhibitors were made and analyzed with inhibition assays against both the wt protease and D168A, a mutant. No inhibitor was found to be more potent than MK-5172, however one (WK-27) was found to have very similar Ki values and further study of it could lead to more refined drug design

SUSTAINING ETHICS EDUCATION IN ENGINEERING: A BLENDED APPROACH TO ETHICS INSTRUCTION

Engineering educators face challenges in teaching ethics, such as a lack of training in ethics instruction and finding time for ethics. The aim of this project was to develop a sustainable blended online method for instructing students in how to navigate ethical situations and to compare this method with in-class lectures from trained faculty. The blended method was composed of an online module comprised of a video series featuring trained ethics instructors and an in-class discussion led by the regular professor. Through paired t-testing, the blended approach was found to be as effective as the joint-venture method. With a more widespread approach this method could be used for more than an introduction to ethics, with modules designed to cover ethical issues to a greater extent

Sarcopenia in lung cancer: Could chest imaging help?

Introduction: Fifteen to seventy percent of cancer patients demonstrate sarcopenia.1-6,[i],[ii],[iii],[iv],[v],[vi],[vii],[viii],[ix],[x],[xi],[xii],[xiii] Analysis of iliopsoas cross-sectional area, a non-invasive surrogate measure for sarcopenia in patients with cancer has been associated with survival.[xiv],[xv],[xvi],[xvii] The pectoralis muscle may be a more accessible target for measuring sarcopenia in lung cancer patients,[xviii] but it is not known if it this correlates with iliopsoas cross-sectional area. Since measurements vary, it is most accurate to use internal controls. We attempted to examine the cross-sectional area of the two muscles and any change over the treatment period. Methods: Charts were reviewed in 44 subjects who underwent surgical treatment of lung cancer. Available imaging at pre-treatment, 6 months, and 12 months was reviewed for the cross-sectional area of the pectoralis and the iliopsoas. The cross-sectional area of the pectoralis and the iliopsoas were measured manually at diagnosis by two different researchers, and the pectoralis was measured at 6 months and 12 months in subjects who were treated for lung cancer. Follow-up iliopsoas data was not available. Results: Of the 44 subjects, 13 had a complete set of imaging. The mean age was 66 years old and the mean BMI was 28.72. There were 8 females and 5 males. 12 out of 13 were Caucasian. 12 out of 13 were stage T1 or T2. 12 out of 13 had undergone lobectomy. 10 out of the 13 were at ECOG performance status grade 0 at diagnosis. 4 out of 13 had postoperative events. The mean iliopsoas area at diagnosis was 8.17cm2. The mean pectoralis area at diagnosis was 14.5 cm2. The mean pectoralis area at 6 months was 13.9 cm2. The mean pectoralis area at 12 months was 14.5cm2. 8 out of 13 subjects had a decrease in mean pectoralis area at 6 months and 6 subjects had a decrease at 12 months. Conclusion: There was no significant decrease in cross-sectional area of the pectoralis over the lung cancer treatment period. This could be because of the initial high performance status of our sample, the small size, or sarcopenia occurs comorbidly with presentation. References: [i] Bowden JC, Williams LJ, Simms A, Price A, Campbell S, Fallon MT, Fearon KC. Prediction of 90 day and overall survival after chemoradiotherapy for lung cancer: role of performance status and body composition. Clinical Oncology. 2017 Sep 1;29(9):576-84. [ii] Kim EY, Lee HY, Kim KW, Lee JI, Kim YS, Choi WJ, Kim JH. Preoperative Computed Tomography–Determined Sarcopenia and Postoperative Outcome after Surgery for Non-Small Cell Lung Cancer. Scandinavian Journal of Surgery. 2017 Dec 1:1457496917748221. [iii] Amini N, Spolverato G, Gupta R, Margonis GA, Kim Y, Wagner D, Rezaee N, Weiss MJ, Wolfgang CL, Makary MM, Kamel IR. Impact total psoas volume on short-and long-term outcomes in patients undergoing curative resection for pancreatic adenocarcinoma: a new tool to assess sarcopenia. Journal of Gastrointestinal Surgery. 2015 Sep 1;19(9):1593-602. [iv] Kasatkina E. CT-assessment of sarcopenia as a predictor of post-Whipple complications. European Congress of Radiology 2013. [v] Sabel MS, Lee J, Cai S, Englesbe MJ, Holcombe S, Wang S. Sarcopenia as a prognostic factor among patients with stage III melanoma. Annals of surgical oncology. 2011 Dec 1;18(13):3579-85. [vi] Blauwhoff-Buskermolen S, Versteeg KS, de van der Schueren MA, den Braver NR, Berkhof J, Langius JA, Verheul HM. Loss of muscle mass during chemotherapy is predictive for poor survival of patients with metastatic colorectal cancer. Journal of Clinical Oncology. 2016 Feb 22;34(12):1339-44. [vii] Villaseñor A, Ballard-Barbash R, Baumgartner K, Baumgartner R, Bernstein L, McTiernan A, Neuhouser ML. Prevalence and prognostic effect of sarcopenia in breast cancer survivors: the HEAL Study. Journal of Cancer Survivorship. 2012 Dec 1;6(4):398-406. [viii] Kuroki LM, Mangano M, Allsworth JE, Menias CO, Massad LS, Powell MA, Mutch DG, Thaker PH. Pre-operative assessment of muscle mass to predict surgical complications and prognosis in patients with endometrial cancer. Annals of surgical oncology. 2015 Mar 1;22(3):972-9. [ix] Peng PD, Van Vledder MG, Tsai S, De Jong MC, Makary M, Ng J, Edil BH, Wolfgang CL, Schulick RD, Choti MA, Kamel I. Sarcopenia negatively impacts short‐term outcomes in patients undergoing hepatic resection for colorectal liver metastasis. Hpb. 2011 Jul 1;13(7):439-46. [x] Prado CM, Baracos VE, McCargar LJ, Reiman T, Mourtzakis M, Tonkin K, Mackey JR, Koski S, Pituskin E, Sawyer MB. Sarcopenia as a determinant of chemotherapy toxicity and time to tumor progression in metastatic breast cancer patients receiving capecitabine treatment. Clinical cancer research. 2009 Apr 15;15(8):2920-6. [xi] Reisinger KW, Bosmans JW, Uittenbogaart M, Alsoumali A, Poeze M, Sosef MN, Derikx JP. Loss of skeletal muscle mass during neoadjuvant chemoradiotherapy predicts postoperative mortality in esophageal cancer surgery. Annals of surgical oncology. 2015 Dec 1;22(13):4445-52. [xii] Cushen SJ, Power DG, Murphy KP, McDermott R, Griffin BT, Lim M, Daly L, MacEneaney P, O\u27Sullivan K, Prado CM, Ryan AM. Impact of body composition parameters on clinical outcomes in patients with metastatic castrate-resistant prostate cancer treated with docetaxel. Clinical nutrition ESPEN. 2016 Jun 1;13:e39-45. [xiii] van Vugt JL, Braam HJ, van Oudheusden TR, Vestering A, Bollen TL, Wiezer MJ, de Hingh IH, van Ramshorst B, Boerma D. Skeletal muscle depletion is associated with severe postoperative complications in patients undergoing cytoreductive surgery with hyperthermic intraperitoneal chemotherapy for peritoneal carcinomatosis of colorectal cancer. Annals of surgical oncology. 2015 Oct 1;22(11):3625-31. [xiv] Feliciano EM, Kroenke CH, Meyerhardt JA, Prado CM, Bradshaw PT, Kwan ML, Xiao J, Alexeeff S, Corley D, Weltzien E, Castillo AL. Association of Systemic Inflammation and Sarcopenia With Survival in Nonmetastatic Colorectal Cancer: Results From the C Scans Study. JAMA oncology. 2017 Dec 1;3(12):e172319-. [xv] Prado CM, Lieffers JR, McCargar LJ, Reiman T, Sawyer MB, Martin L, Baracos VE. Prevalence and clinical implications of sarcopenic obesity in patients with solid tumours of the respiratory and gastrointestinal tracts: a population-based study. The lancet oncology. 2008 Jul 1;9(7):629-35. [xvi] Peng P, Hyder O, Firoozmand A, Kneuertz P, Schulick RD, Huang D, Makary M, Hirose K, Edil B, Choti MA, Herman J. Impact of sarcopenia on outcomes following resection of pancreatic adenocarcinoma. Journal of gastrointestinal surgery. 2012 Aug 1;16(8):1478-86. [xvii] Tan BH, Birdsell LA, Martin L, Baracos VE, Fearon KC. Sarcopenia in an overweight or obese patient is an adverse prognostic factor in pancreatic cancer. Clinical cancer research. 2009 Nov 15;15(22):6973-9. [xviii] Go SI, Park MJ, Song HN, Kang MH, Park HJ, Jeon KN, Kim SH, Kim MJ, Kang JH, Lee GW. Sarcopenia and inflammation are independent predictors of survival in male patients newly diagnosed with small cell lung cancer. Supportive Care in Cancer. 2016 May 1;24(5):2075-84

AmphibiCare: Providing Medical Supplies and Urgent Care to South Sudan

South Sudan with its swampy, desolate terrain, has only 50 km of paved roads making it hard to travel and distribute medical supplies to remote areas, which are susceptible to numerous diseases. We have designed a prototype, all-terrain vehicle, that can overcome these harsh terrains[4] . Our prototype was able to traverse simulated terrain similar to that found in South Sudan[2]