Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery.

The recently developed AlphaFold2 (AF2) algorithm predicts proteins' 3D structures from amino acid sequences. The open AlphaFold protein structure database covers the complete human proteome. Using an industry-leading molecular docking method (Glide), we investigated the virtual screening performance of 37 common drug targets, each with an AF2 structure and known holo and apo structures from the DUD-E data set. In a subset of 27 targets where the AF2 structures are suitable for refinement, the AF2 structures show comparable early enrichment of known active compounds (avg. EF 1%: 13.0) to apo structures (avg. EF 1%: 11.4) while falling behind early enrichment of the holo structures (avg. EF 1%: 24.2). With an induced-fit protocol (IFD-MD), we can refine the AF2 structures using an aligned known binding ligand as the template to improve the performance in structure-based virtual screening (avg. EF 1%: 18.9). Glide-generated docking poses of known binding ligands can also be used as templates for IFD-MD, achieving similar improvements (avg. EF 1% 18.0). Thus, with proper preparation and refinement, AF2 structures show considerable promise for in silico hit identification.

Design, synthesis and optimization of bis-amide derivatives as CSF1R inhibitors.

Signaling via the receptor tyrosine kinase CSF1R is thought to play an important role in recruitment and differentiation of tumor-associated macrophages (TAMs). TAMs play pro-tumorigenic roles, including the suppression of anti-tumor immune response, promotion of angiogenesis and tumor cell metastasis. Because of the role of this signaling pathway in the tumor microenvironment, several small molecule CSF1R kinase inhibitors are undergoing clinical evaluation for cancer therapy, either as a single agent or in combination with other cancer therapies, including immune checkpoint inhibitors. Herein we describe our lead optimization effort that resulted in the identification of a potent, cellular active and orally bioavailable bis-amide CSF1R inhibitor. Docking and biochemical analysis allowed the removal of a metabolically labile and poorly permeable methyl piperazine group from an early lead compound. Optimization led to improved metabolic stability and Caco2 permeability, which in turn resulted in good oral bioavailability in mice.

From virtual to clinical: The discovery of PGN-1531, a novel antagonist of the prostanoid EP4 receptor.

In this Letter, we present the results of a hit-finding and lead optimization programme against the EP4 receptor (EP4R). In a short time period, we were able to discover five structurally diverse series of hit compounds using a combination of virtual screening methods. The most favoured hit, compound 6, was demonstrated to be a competitive antagonist of the EP4R. Compound 73 was identified following several rounds of optimization, which centred on improving both the primary EP4R affinity and selectivity against the related EP2R as well as the aqueous solubility. This work culminated in the preparation of PGN-1531, the sodium salt of 73, which showed a marked improvement in solubility (>10 mg/mL). PGN-1531 is a potent and selective antagonist at EP4Rs in vitro and in vivo, with the potential to alleviate the symptoms of migraine that result from cerebral vasodilatation.

It Is "All About Relationships" in Lifestyle Programmes for Adults Living With Type Two Diabetes Underpinned by a Person/Whanau-Centred Care Approach.

Background: Lifestyle programmes are important in the management of type 2 diabetes (T2D). The Diabetes Community Exercise Programme (DCEP) is an exercise and educational programme for adults living with T2D with the aim of enhancing exercise self-efficacy and supporting wellbeing. DCEP is underpinned by a model of person/whanau-centred care and the spirit of Motivational Interviewing. Person-centred care models in the context of rehabilitation and long-term health conditions are still evolving. This paper explores what those involved in DCEP perceived important to its person/whanau-centredness. Method: An evaluative qualitative methodological approach was used with data collected by open-ended interviews and a focus-group at completion of the initial 12-week part of DCEP. Interviews were audio-recorded and transcribed verbatim. Participants were 16 DCEP attendees and 13 healthcare professionals (HCPs) involved in DCEP delivering. Data were analysed using the General Inductive Approach. Results: The three interconnected themes constructed from the analysis were 'It's all about relationships', Balancing the Outside World, and Empowering through Knowledge. Through the experience and motivation of positive person-centred relationships, DCEP addressed attendees' T2D health needs, but they were constantly balancing these needs with those of family, employers, finances, other health needs and life interests. DCEP relationships facilitated ongoing discussions between attendees and between attendees and HCPs. The ability to discuss in a supportive and non-judgmental environment helped attendees to make sense and process the information they gained at DCEP. This empowering through knowledge in turn helped attendees to work out ways of balancing the outside world and thus better address their T2D needs. Conclusion: It is "all about relationships" was key to DCEP's person/whanau-centred approach-all other factors related back to the development and maintenance of relationships. These relationships were between all whanau involved: the attendees, their family, the wider community, the healthcare provider organisations, and the HCPs and personnel involved in delivering DCEPs. These relationships created an accepting, understanding and social atmosphere that enabled attendance and facilitated both knowledge exchange and ability to exercise, both considered to be beneficial by attendees. Importantly, these relationships took time to develop, but the benefits were worth the investment.

Implementation of the Diabetes Community Exercise and Education Programme (DCEP) for the management of type 2 diabetes: qualitative process evaluation.

OBJECTIVES: To examine context-specific delivery factors, facilitators and barriers to implementation of the Diabetes Community Exercise and Education Programme (DCEP) for adults with type 2 diabetes (T2D) using the Reach, Effectiveness, Adoption, Implementation and Maintenance framework. DESIGN: A qualitative evaluation embedded within the DCEP pragmatic randomised controlled trial. Data collected via focus groups and interviews and analysed thematically. SETTING: Community-based in two cities (Dunedin and Invercargill) in the lower south island of New Zealand. PARTICIPANTS: Seventeen adults diagnosed with T2D attending DCEP and 14 healthcare professionals involved in DCEP delivery. INTERVENTION: DCEP is a twice weekly session of exercise and education over 12 weeks, followed by a twice weekly ongoing exercise class. RESULTS: While our reach target was met (sample size, ethnic representation), the randomisation process potentially deterred Maori and Pasifika from participating. The reach of DCEP may be extended through the use of several strategies: promotion of self-referral, primary healthcare organisation ownership and community champions. DCEP was considered effective based on perceived benefit. The social and welcoming environment created relationships and connections. People felt comfortable attending DCEP and empowered to learn. Key to implementation and adoption was the building of trusting relationships with local health providers and communities. This takes time and care and cannot be rushed. Training of staff and optimising communication needed further attention. To maintain DCEP, delivery close to where people live and a generic approach catering for people with multiple chronic conditions may be required. CONCLUSIONS: For success, lifestyle programmes such as DCEP, need time and diligence to build and maintain networks and trust. Beyond frontline delivery staff and target populations, relationships should extend to local healthcare organisations and communities. Access and ongoing attendance are enabled by healthcare professionals practicing in a nuanced person-centred manner; this, plus high staff turnover, necessitates ongoing training. TRIAL REGISTRATION NUMBER: ACTRN12617001624370.

Viral inhibition assay: a CD8 T cell neutralization assay for use in clinical trials of HIV-1 vaccine candidates.

We have characterized an assay measuring CD8 T cell-mediated inhibition of human immunodeficiency virus (HIV) type 1 replication, demonstrating specificity and reproducibility and employing a panel of primary HIV-1 isolates. The assay uses relatively simple autologous cell culture and enzyme-linked immunosorbent assay, avoids generation of T cell clones, and can be performed with <2 million peripheral blood mononuclear cells. Efficient CD8 T cell-mediated cross-clade inhibition of HIV-1 replication in vitro was demonstrated in antiretroviral therapy-naive HIV-1-infected subjects with controlled viral replication in vivo but not in viremic subjects. An HIV-1 vaccine candidate, consisting of DNA and recombinant adenovirus 5 vectors tested in a phase I clinical trial, induced CD8 T cells that efficiently inhibited HIV-1 in a HLA-I-dependent manner. Assessment of direct antiviral T cell function by this assay provides additional information to guide vaccine design and the prioritizing of candidates for further clinical trials.

Long Term Exercise Engagement of Adults Living With Type Two Diabetes Is Enhanced by a Person-Centred Care Approach Delivered by Knowledgeable, Well Trained Health Care Professionals.

Background: Regular engagement in exercise or physical activity is a key evidence-based recommendation in the self-management of type 2 diabetes (T2D). The Diabetes Community Exercise Programme (DCEP) is an exercise and educational programme aimed at supporting adults living with T2D to take control of their health and to live well with T2D. It was specifically developed to enhance the self-efficacy of people to engage in exercise for a long term and is underpinned by the spirit of motivational interviewing. This study explores what DCEP attendees and health care professionals (HCPs) who deliver the programme perceived DCEP to be and what motivated attendance. Such insights further the knowledge of how people with T2D can be supported to engage in exercise or physical activity programmes. Method: This qualitative study used open-ended interviews of 17 DCEP attendees and 12 HCPs delivering DCEP. Interviews occurred at the completion of the initial twice-a-week, 12-week duration part of the programme and prior to attendees starting with a twice-weekly maintenance exercise class, which forms the second part of the programme. Interviews were audio-recorded, transcribed verbatim and analysed with the General Inductive Approach. Results: The two themes constructed from the analysis were person-centred care and attention to logistics and administration. Person-centred care comprised four subthemes: monitoring, individualised exercise within a sociable group setting, flexible education and discussion, and HCP training, and these components appeared to support attendees to engage in exercise. The second theme spoke about the processes, that was either present or that should be included, that enabled DCEP delivery, such as appropriate venues, flexible approaches to time of day and the requirement of good administrative support. Conclusion: The Diabetes Community Exercise Programme did motivate people with T2D to engage in exercise. Important to this was the emphasis on a person-centred approach that focussed on the health status monitoring and educational and social aspects of the programme, which in turn facilitated exercise engagement. Knowledgeable HCPs who require training in the delivery of person-centred care to tailor the exercise and education to the individual is imperative. Equally important are optimal exercise environments and well-trained administrative support.

Identification and hit-to-lead exploration of a novel series of histamine H4 receptor inverse agonists.

The identification and hit-to-lead exploration of a novel, potent and selective series of histamine H(4) receptor inverse agonists is described. The initial hit, 3A (IC(50) 19 nM) was identified by means of a ligand-based virtual screening approach. Subsequent medicinal chemistry exploration yielded 18I which possessed increased potency (R-enantiomer IC(50) 1 nM) as well as enhanced microsomal stability.

Discovery of Potent, Selective, and Orally Bioavailable Inhibitors of USP7 with In Vivo Antitumor Activity.

USP7 is a promising target for cancer therapy as its inhibition is expected to decrease function of oncogenes, increase tumor suppressor function, and enhance immune function. Using a structure-based drug design strategy, a new class of reversible USP7 inhibitors has been identified that is highly potent in biochemical and cellular assays and extremely selective for USP7 over other deubiquitinases. The succinimide was identified as a key potency-driving motif, forming two strong hydrogen bonds to the allosteric pocket of USP7. Redesign of an initial benzofuran-amide scaffold yielded a simplified ether series of inhibitors, utilizing acyclic conformational control to achieve proper amine placement. Further improvements were realized upon replacing the ether-linked amines with carbon-linked morpholines, a modification motivated by free energy perturbation (FEP+) calculations. This led to the discovery of compound 41, a highly potent, selective, and orally bioavailable USP7 inhibitor. In xenograft studies, compound 41 demonstrated tumor growth inhibition in both p53 wildtype and p53 mutant cancer cell lines, demonstrating that USP7 inhibitors can suppress tumor growth through multiple different pathways.

Active symptom control with or without chemotherapy in the treatment of patients with malignant pleural mesothelioma (MS01): a multicentre randomised trial.

BACKGROUND: Malignant pleural mesothelioma is almost always fatal, and few treatment options are available. Although active symptom control (ASC) has been recommended for the management of this disease, no consensus exists for the role of chemotherapy. We investigated whether the addition of chemotherapy to ASC improved survival and quality of life. METHODS: 409 patients with malignant pleural mesothelioma, from 76 centres in the UK and two in Australia, were randomly assigned to ASC alone (treatment could include steroids, analgesic drugs, bronchodilators, palliative radiotherapy [n=136]); to ASC plus MVP (four cycles of mitomycin 6 mg/m2, vinblastine 6 mg/m2, and cisplatin 50 mg/m2 every 3 weeks [n=137]); or to ASC plus vinorelbine (one injection of vinorelbine 30 mg/m2 every week for 12 weeks [n=136]). Randomisation was done by minimisation, with stratification for WHO performance status, histology, and centre. Follow-up was every 3 weeks to 21 weeks after randomisation, and every 8 weeks thereafter. Because of slow accrual, the two chemotherapy groups were combined and compared with ASC alone for the primary outcome of overall survival. Analysis was by intention to treat. This study is registered, number ISRCTN54469112. FINDINGS: At the time of analysis, 393 (96%) patients had died (ASC 132 [97%], ASC plus MVP 132 [96%], ASC plus vinorelbine 129 [95%]). Compared with ASC alone, we noted a small, non-significant survival benefit for ASC plus chemotherapy (hazard ratio [HR] 0.89 [95% CI 0.72-1.10]; p=0.29). Median survival was 7.6 months in the ASC alone group and 8.5 months in the ASC plus chemotherapy group. Exploratory analyses suggested a survival advantage for ASC plus vinorelbine compared with ASC alone (HR 0.80 [0.63-1.02]; p=0.08), with a median survival of 9.5 months. There was no evidence of a survival benefit with ASC plus MVP (HR 0.99 [0.78-1.27]; p=0.95). We observed no between-group differences in four predefined quality-of-life subscales (physical functioning, pain, dyspnoea, and global health status) at any of the assessments in the first 6 months. INTERPRETATION: The addition of chemotherapy to ASC offers no significant benefits in terms of overall survival or quality of life. However, exploratory analyses suggested that vinorelbine merits further investigation.

Protocol for a randomised controlled trial to evaluate the effectiveness of the diabetes community exercise and education programme (DCEP) for long-term management of diabetes.

INTRODUCTION: Type 2 diabetes is common in Maori and Pacific peoples and in those living in areas of high socioeconomic deprivation in New Zealand (NZ). People with type 2 diabetes often have multimorbidity, which makes their diabetes management more complex. The Diabetes Community Exercise and Education Programme (DCEP) is an interprofessional, patient-centred, whanau (family)-supported package of care specifically developed to engage with Maori and Pacific people and those living in deprived areas. We have previously demonstrated the feasibility and acceptability of the DCEP. This study aims to determine the effectiveness and cost-effectiveness of the DCEP through a pragmatic randomised controlled trial (RCT). METHODS AND ANALYSIS: 220 adults (age ≥35 years) with type 2 diabetes will be recruited from general practices in the lower South Island of NZ (Dunedin and Invercargill) to participate in an RCT. Participants will be randomised to intervention (DCEP) and control (usual care) groups. The DCEP participants will have their exercise goals agreed on with a physiotherapist and nurse and will attend two 90 min exercise and education sessions per week for 12 weeks. The primary outcome measure is blood glucose control (glycated haemoglobin). Secondary outcome measures include quality of life assessed using the Audit of Diabetes-Dependent Quality of Life questionnaire. Data will be collected at four time points: baseline, end of the 12-week intervention (3 months), 6 months postintervention (9 months) and 12 months after the intervention ends (15 months). We will also conduct a cost-effectiveness analysis and a qualitative process evaluation. ETHICS AND DISSEMINATION: The study has been approved by the Health and Disability Ethics Committee, Ministry of Health (HDEC17/CEN/241/AM01). A key output will be the development of an evidence-based training package to facilitate implementation of the DCEP in other NZ regions. TRIAL REGISTRATION NUMBER: ACTRN 12617001624370 p; Pre-results.

Pharmacokinetics and pharmacodynamics of the nucleoside sparing dual regimen containing rilpivirine plus darunavir/ritonavir in treatment-naïve HIV-1-infected individuals.

BACKGROUND: We aimed at investigating the antiviral activity and the pharmacokinetics of the dual antiretroviral (ARV) combination of rilpivirine plus darunavir/ritonavir 25/800/100 mg once-daily in naïve HIV-1-infected individuals (NHII) with different baseline viral loads. SETTINGS: Pharmacokinetic/pharmacodynamics study in ARV-naïve HIV-infected individuals. METHODS: The primary endpoint was the number of NHII with HIV-RNA < 40 copies/mL at week 48. Secondary endpoints included rilpivirine/darunavir/ritonavir pharmacokinetics, HIV-RNA decay, and changes in ECG QT interval. RESULTS: Thirty-six individuals were enrolled, 18 with a baseline viral load < 100,000 copies/mL (group A) and 18 with a baseline viral load > 100,000 copies/mL (group B). All but 1 (HIV-RNA = 63 copies/mL) subjects achieved viral load < 50 copies/mL by week 36, and all at week 48. Median (range) HIV-RNA reduction (Log10 copies/mL) was 1.3 (0.6-1.9) over the first week, with no differences between groups A and B. Geometric mean and 95%CI rilpivirine Cmax, Ctrough, AUC were 183 (165-239), 114 (104-109) ng/mL, 2966 (2704-3820) ng h/mL. No QTcF interval changes were recorded. CONCLUSIONS: rilpivirine/darunavir/ritonavir could be efficacious, with limited short-term toxicity in ARV-naïve patients. Although rilpivirine was co-administered with ritonavir, its exposure was within ranges measured during phase III trials.

An open-label, randomized comparative pilot study of a single-class quadruple therapy regimen versus a 2-class triple therapy regimen for individuals initiating antiretroviral therapy.

OBJECTIVE: To examine the antiviral potency and tolerability profile of a single-class four drug (quadruple) nucleoside reverse transcriptase inhibitor (NRTI) regimen compared with a 2-class standard-of-care regimen. METHODOLOGY: A three-centre, randomized, open-label comparative pilot study of zidovudine/lamivudine/efavirenz (triple) versus abacavir/lamivudine/zidovudine/tenofovir (quadruple) therapy in HIV-1-infected, treatment-naive individuals. Both regimens were taken without regard to food and consisted of a twice-daily regimen and 3 pills/day. The study power was based on time-weighted average changes in HIV-1 RNA load. RESULTS: A total of 114 individuals (56 triple, 57 quadruple) received at least one dose of medication. Patients were well matched at baseline for viral load (mean 5.26 log10 versus 5.13 log10, respectively) and CD4 cell count (median 193 versus 153 cells/mm3, respectively). The two regimens performed similarly with regards to all endpoints. At week 48, by intention-to-treat, missing=failure analysis, 68% of triple- and 67% of quadruple-drug treated patients had an HIV-1 RNA <50copies/ml (P>0.05). On-treatment analysis showed 40/40 (100%) of triple- and 39/40 (97.5%) of quadruple-drug treated patients (P=0.996) had responded to <50copies/ml. No unexpected adverse events were reported. Changes in total cholesterol and triglycerides were modest but significantly favoured the quadruple therapy regimen at multiple time points. CONCLUSION: This pilot study suggests a quadruple NRTI-based regimen provides similar antiviral potency, tolerability and administrative characteristics to a 2-class triple therapy regimen. These findings should be confirmed in a more fully powered study. Potent quadruple NRTI-based regimens may have advantages for some individuals with regards to salvageability, tolerability and drug interactions.

A virtual screening approach to finding novel and potent antagonists at the melanin-concentrating hormone 1 receptor.

Melanin-concentrating hormone (MCH) has been known to be an appetite-stimulating peptide for a number of years. However, it is only recently that MCH has been discovered to be the natural ligand for a previously "orphan" G-protein-coupled receptor, now designated MCH-1R. This receptor has been shown to mediate the effects of MCH on appetite and body weight, and consequently, drug discovery programs have begun to exploit this information in the search for MCH-1R antagonists for the treatment of obesity. In this paper, we report the rapid discovery of multiple, structurally distinct series of MCH-1R antagonists using a variety of virtual screening techniques. The most potent of these compounds (12) demonstrated an IC(50) value of 55 nM in the primary screen and exhibited antagonist properties in a functional cellular assay measuring Ca(2+) release. More potent compounds were identified by follow-up searches around the initial hit. A proposed binding mode for compound 12 in a homology model of the MCH-1R is also presented.

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor.

A series of triazolylpurine analogues show interesting and unintuitive structure-activity relationships against the A2A adenosine receptor. As the 2-substituted aliphatic group is initially increased to methyl and isopropyl, there is a decrease in potency; however, extending the substituent to n-butyl and n-pentyl results in a significant gain in potency. This trend cannot be readily explained by ligand-receptor interactions, steric effects, or differences in ligand desolvation. Here, we show that a novel method for characterizing solvent thermodynamics in protein binding sites correctly predicts the trend in binding affinity for this series based on the differential water displacement patterns. In brief, small unfavorable substituents occupy a region in the A2A adenosine receptor binding site predicted to contain stable waters, while the longer favorable substituents extend to a region that contains several unstable waters. The predicted binding energies associated with displacing water within these hydration sites correlate well with the experimental activities.

Lack of pharmacokinetic drug interaction between tenofovir disoproxil fumarate and nelfinavir mesylate.

A study explored the pharmacokinetics of tenofovir (300 mg administered once daily) and nelfinavir (1,250 mg twice daily) when coadministered in 29 healthy volunteers. Tenofovir, nelfinavir, and M8 pharmacokinetics was unaltered when tenofovir and nelfinavir were coadministered, and tenofovir administration did not affect the M8/nelfinavir area under the concentration-versus-time curve over the dosing interval (AUC(tau)) ratio. No interaction between tenofovir and nelfinavir was observed.