Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS).

A simple-to-implement and experimentally validated computational workflow for sequence modification of peptide inhibitors of protein-protein interactions (PPIs) is described.

Query-guided protein-protein interaction inhibitor discovery.

Protein-protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein-protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a ß-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low µM activity as determined by a combination of fluorescence anisotropy and 1H-15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure-activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.

Stapled Peptides as HIF-1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency.

Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1α) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1α/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an α-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive α-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.

Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces.

Protein-protein interactions (PPIs) are vital to all biological processes. These interactions are often dynamic, sometimes transient, typically occur over large topographically shallow protein surfaces, and can exhibit a broad range of affinities. Considerable progress has been made in determining PPI structures. However, given the above properties, understanding the key determinants of their thermodynamic stability remains a challenge in chemical biology. An improved ability to identify and engineer PPIs would advance understanding of biological mechanisms and mutant phenotypes and also provide a firmer foundation for inhibitor design. In silico prediction of PPI hot-spot amino acids using computational alanine scanning (CAS) offers a rapid approach for predicting key residues that drive protein-protein association. This can be applied to all known PPI structures; however there is a trade-off between throughput and accuracy. Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an α-helix-mediated PPI), SIMS/SUMO, and GKAP/SHANK-PDZ (both ß-strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-spot residues at a topographically novel Affimer/BCL-xL protein-protein interface.

Supramolecular Self-Sorting Networks using Hydrogen-Bonding Motifs.

A current objective in supramolecular chemistry is to mimic the transitions between complex self-sorted systems that represent a hallmark of regulatory function in nature. In this work, a self-sorting network, comprising linear hydrogen motifs, was created. Selecting six hydrogen-bonding motifs capable of both high-fidelity and promiscuous molecular recognition gave rise to a complex self-sorting system, which included motifs capable of both narcissistic and social self-sorting. Examination of the interactions between individual components, experimentally and computationally, provided a rationale for the product distribution during each phase of a cascade. This reasoning holds through up to five sequential additions of six building blocks, resulting in the construction of a biomimetic network in which the presence or absence of different components provides multiple unique pathways to distinct self-sorted configurations.

Hep-CORE: a cross-sectional study of the viral hepatitis policy environment reported by patient groups in 25 European countries in 2016 and 2017.

INTRODUCTION: The first World Health Organization (WHO) global health sector strategy on hepatitis B and C viruses (HBV and HCV) has called for the elimination of viral hepatitis as a major public health threat by 2030. This study assesses policies and programmes in support of elimination efforts as reported by patient groups in Europe. METHODS: In 2016 and 2017, hepatitis patient groups in 25 European countries participated in a cross-sectional survey about their countries' policy responses to HBV and HCV. The English-language survey addressed overall national response; public awareness/engagement; disease monitoring; prevention; testing/diagnosis; clinical assessment; and treatment. We performed a descriptive analysis of data and compared 2016 and 2017 findings. RESULTS: In 2017, 72% and 52% of the 25 European study countries were reported to not have national HBV and HCV strategies respectively. The number of respondents indicating that their governments collaborated with civil society on viral hepatitis control increased from 13 in 2016 to 18 in 2017. In both 2016 and 2017, patient groups reported that 9 countries (36%) have disease registers for HBV and 11 (44%) have disease registers for HCV. The number of countries reported to have needle and syringe exchange programmes available in all parts of the country dropped from 10 (40%) in 2016 to 8 in 2017 (32%). In both 2016 and 2017, patient groups in 5 countries (20%) reported that HCV treatment is available in non-hospital settings. From 2016 to 2017, the reported number of countries with no restrictions on access to direct-acting antivirals for HCV increased from 3 (12%) to 7 (28%), and 5 fewer countries were reported to refuse treatment to people who are currently injecting drugs. CONCLUSIONS: The patient-led Hep-CORE study offers a unique perspective on the readiness of study countries to undertake comprehensive viral hepatitis elimination efforts. Viral hepatitis monitoring should be expanded to address policy issues more comprehensively and to incorporate civil society perspectives, as is the case with global HIV monitoring. Policy components should also be explicitly added to the WHO framework for monitoring country-level progress against viral hepatitis.

Health Outcomes for Clients of Needle and Syringe Programs in Prisons.

High levels of drug dependence have been observed in the prison population globally, and the sharing of injecting drug equipment in prisons has contributed to higher prevalence of bloodborne diseases in prisoners than in the general population. Few prison needle and syringe programs (PNSPs) exist. We conducted a systematic review to assess evidence regarding health outcomes of PNSPs. We searched peer-reviewed databases for data relating to needle and syringe programs in prisons. The search methodology was conducted in accordance with accepted guidelines. Five studies met review inclusion criteria, and all presented evidence associating PNSPs with one or more health benefits, but the strength of the evidence was low. The outcomes for which the studies collectively demonstrated the strongest evidence were prevention of human immunodeficiency virus and viral hepatitis. Few negative consequences from PNSPs were observed, consistent with previous evidence assessments. More research is needed on PNSP effectiveness, and innovative study designs are needed to overcome methodological limitations of previous research. Until stronger evidence becomes available, policymakers are urged to recognize that not implementing PNSPs has the potential to cause considerable harm, in light of what is currently known about the risks and benefits of needle and syringe programs and PNSPs and about the high prevalence of human immunodeficiency virus and viral hepatitis in prisons.

Policy responses to hepatitis C in the Nordic countries: Gaps and discrepant reporting in the Hep-Nordic study.

BACKGROUND AND AIMS: In the Nordic countries (Denmark, Finland, Iceland, Norway, Sweden), the prevalence of chronic hepatitis C virus (HCV) infection is relatively low in the general population, but is much higher among people who inject drugs (PWID). We conducted an exploratory study to investigate the extent to which these countries have policies supporting key elements of the public health response that is necessary to achieve the global goal of eliminating HCV as a public health threat. METHODS: Fourteen stakeholders representing government agencies, medical societies, and civil society organisations (CSOs) in the Nordic countries completed a cross-sectional online survey that included 21 policy questions related to national coordination, prevention, testing, linkage to care, and treatment. We summarised the findings in a descriptive analysis, and noted discrepant responses from stakeholders within the same country. RESULTS: Stakeholders reported that three of the five study countries have national viral hepatitis strategies, while only Iceland has a national HCV elimination goal. The availability of harm reduction services varies, with opioid substitution therapy provided for the general population throughout all countries, but not needle and syringe programmes. No country has access to anonymous HCV testing in all parts of the country. National HCV treatment guidelines are available in all countries except Finland, and all countries provide publicly funded direct-acting antiviral treatment. Disagreement regarding policies was observed across countries, and CSOs were the stakeholder group that most frequently answered survey questions incorrectly. CONCLUSION: The Nordic region as a whole has not consistently expressed its commitment to tackling HCV, despite the existence of large HCV epidemics among PWID in these countries. Stakeholder alignment and an established elimination goal with an accompanying strategy and implementation plan should be recognised as the basis for coordinated national public health efforts to achieve HCV elimination in the Nordic region and elsewhere.

Alkaline phosphatase variation during carfilzomib treatment is associated with best response in multiple myeloma patients.

The ubiquitin-proteasome pathway regulates bone formation through osteoblast differentiation. We analyzed variation alkaline phosphatase (ALP) during carfilzomib treatment. Data from 38 patients enrolled in the PX-171-003 and 29 patients in PX-171-004 studies, for patients with relapsed/refractory myeloma, were analyzed. All patients received 20 mg/m(2) of carfilzomib on Days 1, 2, 8, 9, 15, and 16 of a 28-day cycle. Sixty-seven patients from ALP data were evaluable. In PX-171-003, the ORR (>PR) was 18% and the clinical benefit response (CBR; >MR) was 26%, while in PX-171-004, the ORR was 35.5% overall and 57% in bortezomib-naive patients. ALP increment from baseline was statistically different in patients who achieved ≥ VGPR compared with all others on Days 1 (P = 0.0049) and 8 (P = 0.006) of Cycle 2. In patients achieving a VGPR or better, ALP increased more than 15 units per liter at Cycle 2 Day 1 over baseline. An ALP increase over the same period of time was seen in 26%, 13% and 11% of patients achieving PR, MR, and SD, respectively. This retrospective analysis of patients with relapsed or refractory myeloma treated with single-agent carfilzomib indicates that early elevation in ALP is associated with subsequent myeloma response.