The case for open?access chemical biology | EMBO Reports

Although the creation of new chemical entities has always been considered the realm of patents, I think that it is time for change. Novel chemical tools, most of which will not have drug?like properties, are too valuable to be restricted; they will be of far greater benefit to research if freely available without restrictions on their use. Chemical biologists would benefit from the many advantages that the open consortium model brings: rapid access to research tools; less bureaucratic workload to enter legal agreements; the ability to work with the best people through collaborations focused on the publication of results; and freedom to operate for companies, harnessing the synergies between academic freedom and industrial approaches to systematically tackle a scientific challenge. My call for open?access chemistry public–private partnerships might sound impractical, but pilot projects are already underway….The SGC is a one example of an open public–private partnership. It was created as a legal charity in 2004 to determine the three?dimensional high?resolution structures of medically important proteins. As an open consortium, the resulting structures are placed in the public domain without restriction on their use. The SGC was conceived nearly ten years ago, based on the conviction that high?quality structural information is of tremendous value in promoting drug discovery and a belief that patenting protein structures could limit the freedom to operate for academic and industrial organizations….Although it is clear that open?access chemistry is in the best interests of society, the challenge is the cost. My arguments can be defended on the macroeconomic level, but costs for assay development and for chemical screening and synthesis are incurred locally, by the institutions and from the public purse. Free release of chemical probes by academia would ultimately benefit the pharmaceutical industry and society, but the possibilities for royalty and license payments for universities would decrease. One solution is to explore models in which both the public and private sectors contribute up?front in return for unrestricted access to the results and compounds, as in the SGC. It should also be noted that an open?access model is not in conflict with the aim to commercialize, at least not in the long term. It could be argued that experience built around specific biological systems would allow commercial development at a later stage if findings by the community indicate that a particular protein or pathway is a valid target. A chemical biology centre with such experience would be in an ideal position to develop new chemistry and launch a proprietary programme….

Open access chemical and clinical probes to support drug discovery : Article : Nature Chemical Biology

“Drug discovery resources in academia and industry are not used efficiently, to the detriment of industry and society. Duplication could be reduced, and productivity could be increased, by performing basic biology and clinical proofs of concept within open access industry-academia partnerships. Chemical biologists could play a central role in this effort….In summary, the development of new medicines is being hindered by the way in which academia and industry advance innovative targets. By generating freely available chemical and clinical probes and performing open-access science, the overall system will produce a wider range of clinically validated targets for the same total resource. This is arguably the most effective way to spur the development of treatments for unmet needs.”

Open-source science to enable drug discovery

“The drug discovery process is losing productivity to the detriment of the global economy and human health. The greatest productivity gains in the sector can be achieved by solving the fundamental scientific problems limiting the progression of compounds through clinical trials. These problems must be addressed through a combination of ‘blue sky’ and targeted research on priority issues, perhaps defined within a ‘grand challenges’ framework. For many reasons, targeted research should be performed in PPPs [public–private partnerships] that release information into the public domain immediately, with no restriction on use.”

Bermuda Principles meet structural biology : Article : Nature Structural & Molecular Biology

“The Structural Genomics Consortium (SGC; http://www.thesgconline.org/) is a public-private partnership that places the three-dimensional structures of proteins of relevance to human health into the public domain without restriction on use. Over the past 3 years, the SGC has deposited the structures of more than 550 proteins from its Target List (http://www.thesgconline.org/structures/about.php) into the Protein DataBank (PDB); this accounts for about one-quarter of the new structures of human proteins in the PDB over this period (‘new’ is defined as <95% sequence identity to proteins whose structures were already available in the PDB) and the majority of the new structures from the human parasites that cause malaria, cryptosporidiosis and toxoplasmosis. Over the next 4 years, the SGC is committing to determining the structures of another 600 proteins from its Target List, including eight human integral membrane proteins.

The SGC has been releasing the coordinates for all the SGC structures into the PDB immediately after they meet the SGC quality criteria (http://www.thesgconline.org/structures/sgc_structure_criteria.php), even if the ultimate intention is to describe the work in the peer-reviewed literature. This data release policy, which has often meant that coordinates were available for several months before the manuscript was even written, has not limited the ability of our scientists to publish….”

SGC | Structural Genomics Consortium

“The SGC is engaged in pre-competitive research to facilitate the discovery of new medicines. As part of its mission the SGC is generating reagents and knowledge related to human proteins and proteins from human parasites. The SGC believes that its output will have maximal benefit if released into the public domain without restriction on use, and thus has adopted the following Open Access policy.

The SGC and its scientists are committed to making their research outputs (materials and knowledge) available without restriction on use. This means that the SGC will promptly place its results in the public domain and will not agree to file for patent protection on any of its research outputs. It will seek the same commitment from any research collaborator….”

Comparison between publicly accessible publications, registries and protocols of phase III trials indicated persistence of selective outcome reporting – Journal of Clinical Epidemiology

Abstract:  Objectives

The decision to make protocols of phase III randomized clinical trials (RCTs) publicly accessible by leading journals was a landmark event in clinical trial reporting. Here we compared primary outcomes defined in protocols with those in publications describing the trials, and in trial registration.

 

Study design and setting

We identified phase III RCTs published between January 1, 2012 and June 30, 2015 in The New England Journal of Medicine, The Lancet, The Journal of the American Medical Association and The BMJ with available protocols. Consistency in primary outcomes between protocols and registries (articles) were evaluated.

 

Results

We identified 299 phase III RCTs with available protocols in this analysis. Out of them, 25(8.4%) trials had some discrepancy for primary outcomes between publications and protocols. Types of discrepancies included protocol-defined primary outcome reported as non-primary outcome in publication (11 trials, 3.7%), protocol-defined primary outcome omitted in publication (10 trials, 3.3%), new primary outcome introduced in publication (8 trials, 2.7%), protocol-defined non-primary outcome reported as primary outcome in publication (4 trials, 1.3%) and different timing of assessment of primary outcome (4 trials, 1.3%). Out of trials with discrepancies in primary outcome, 15 trials (60.0%) had discrepancies that favored statistically significant results. Registration could be seen as a valid surrogate of protocol in 237 of 299 trials (79.3%) with regard to primary outcome.

 

Conclusions

Despite unrestricted public access to protocols, selective outcome reporting persists in a small fraction of phase III RCTs. Only studies from four leading journals were included, which may cause selection bias and limit the generalizability of this finding.

NOT-OD-16-149: NIH Policy on the Dissemination of NIH-Funded Clinical Trial Information

“The National Institutes of Health (NIH) is issuing this policy to promote broad and responsible dissemination of information from NIH-funded clinical trials through ClinicalTrials.gov.  The policy establishes the expectation that all investigators conducting clinical trials funded in whole or in part by the NIH will ensure that these trials are registered at ClinicalTrials.gov, and that results information of these trials is submitted to ClinicalTrials.gov.  The policy is complementary to the statutory and regulatory reporting requirements. …”

WHO | Joint statement on public disclosure of results from clinical trials

“The signatories of this joint statement affirm that the prospective registration and timely public disclosure of results from all clinical trials is of critical scientific and ethical importance. Furthermore timely results disclosure reduces waste in research, increases value and efficiency in use of funds and reduces reporting bias, which should lead to better decision-making in health.

Within 12 months of becoming a signatory of this statement, we each pledge to develop and implement a policy with mandated timeframes for prospective registration and public disclosure of the results of clinical trials that we fund, co-fund, sponsor or support. We each agree to monitor registration and endorse the development of systems to monitor results reporting on an ongoing basis. We agree to share challenges and progress in the monitoring of these policies. We agree that transparency is important and therefore the outputs from the monitoring process will be publicly available….”

Sharing by Law: Open Science Takes a Legal Approach

“‘A partnership between the Structural Genomics Consortium (SGC) at the University of Toronto and U of T’s Faculty of Law has yielded a new concept that could change the way scientists share research tools. Aled Edwards, who leads the SGC, is lead author of a recent paper that applies the concept of a legal trust to open research reagents ­— substances that scientists use to test biological hypotheses and give insight into potential new therapies. Under this model, the researchers who receive reagents would become ‘trustees’ obligated to treat the materials as public goods. The article is published in Science Translational Medicine….Academic researchers use public funds to create reagents to use the lab. Currently any reagent created at any University is legally the property of the institution and is shared only under contract. Although this is the status quo, many of us believe science shouldn’t belong to an institution or an individual, but to society and that our work should be viewed as a public good,’ says Edwards, who is also a professor in the Departments of Medical Biophysics and Molecular Genetics and an expert in open science drug discovery.”

Open Pharma – Innovations in medical publishing

“Although scientific publishing is changing fast, most pharma-sponsored research continues to be published through a traditional route of peer-reviewed journals. The current route is slow, with limited transparency and restricted access to research outputs. This has a negative impact on biomedical research and, ultimately, patient healthcare.

Many groups are discussing the future of scientific publishing but, so far, the pharmaceutical industry has provided limited input into the discussions. With half of all biomedical research funding coming from industry, and with substantial issues of trust and transparency still to be addressed, our group thinks not only that industry should be involved in the discussions but also that it should help to drive change. Non-pharmaceutical-industry funders such as the Wellcome Trust and the Bill & Melinda Gates Foundation have been the main drivers of innovation so far. It’s time for the pharmaceutical industry to join them….”