Comparative Structural Genomics on Viral Enzymes involved in Replication
The VIZIER project aims to impact the antiviral drug-design field through the identification of potential new drug targets against RNA viruses and their use in a comprehensive structural characterisation of a diverse set of viruses. The common strategies used for the development of antiviral drugs are mainly based on the knowledge accumulated through studies of virus genetics and structure. The VIZIER project proposes to fill the existing gap between the necessary scientific characterisation of emerging viruses and preclinical drug evaluation.
RNA viruses include more than 350 different major human pathogens and most of the aetiological agents of emerging diseases: viruses of gastroenteritis (more than 1 million deaths annually), measles (more than 45 million cases and 600 000 deaths annually), influenza (more than 100 million cases annually), dengue fever (approximately 300 million cases annually), enteroviruses and encephalitis (several million cases of meningitis annually), hepatitis C virus (more than 170 million infected people in the world).
The Severe Acute Respiratory Syndrome (SARS) outbreak has dramatically demonstrated how high the economic cost of an epidemic caused by an emerging virus could be. This negative impact is actually widening every day, as many governments are forced to make costly arrangements to cope with the threat of bio-terrorism, which lists some deadly RNA viruses in its arsenal. To meet these challenges, science needs to look for new therapeutic and prophylactic substances active against RNA viruses, since those currently available are scarce and of poor potency.
The common strategies used for the development of antiviral drugs are mainly based on the knowledge accumulated through studies of virus genetics and structure. Yet, it is a strange paradox that genomic and structural characterisation of RNA viruses was not accepted as a priority until very recently. The VIZIER project proposes to fill the existing gap between the necessary scientific characterisation of emerging viruses and preclinical drug evaluation.[+] Read More
To address society's needs, scientists need to anticipate potential threats in order to be ready should they arise. The participants of the VIZIER project have created a team that brings together the leading authorities on RNA viruses available in the EU or elsewhere, as well as many leading European structural biologists. This team includes three partners with P4 facilities and leaders in the field of structural genomics. The development of protocols for high-throughput (HTP) protein production means that a concerted programme of structure determination is now appropriate and feasible.
Because they are both the most likely to emerge and the most prone to genetic variability, RNA viruses constitute the main VIZIER targets. These virus classes use profoundly different replicative mechanisms driven by poorly characterised replication machineries. Although virus-specific, the latter are the most conserved and essential viral components and, thus, the most attractive targets for antiviral therapy.
In the framework of this project, the core enzymes/proteins of the replication machinery carefully selected among 300 different RNA viruses, including strains of medical interest, will be characterised. One unique feature of VIZIER, compared to other structural genomics projects, is the integration of a major structural effort within a broad multidisciplinary study, having virology upstream and target validation (candidate drug design) downstream.
As a result, the implementation plan of the VIZIER project is structured into five interacting scientific sections: (1) bioinformatics, for genome annotation, target selection and data integration; (2) virus production and genome sequencing; (3) HTP protein production; (4) HTP crystallisation and structural determination; and (5) target validation to assess the function of enzymes and design strategies for virus inhibition. VIZIER rounds off the plan with training, implementation and dissemination. This organisation will allow the full characterisation, in record time, of a viral target that can quickly be used to design drugs, either by the pharmaceutical industry through the VIZIER Industrial Platform, or by any R&D institution.
VIZIER will produce an unprecedented wealth of data on the replicases of RNA viruses with a window into antiviral drug development. A representative set of RNA-based viruses that belong to three major classes, profoundly different in their replicative strategies, will be characterised by a concerted and multidisciplinary effort unparalleled to date. At the end of this programme, the percentage of sequenced genomes of RNA virus species that infect vertebrates will virtually double from 30% to 55%.
As an example, the genomic characterisation of Flavivirus (ssRNA+) and Arenavirus (ssRNA-) genera, which include a large number of human pathogens, will be systematically achieved. A dramatic advancement is expected in the number and diversity of 3-D structures of the replicative subunits, now in the one-digit range. VIZIER will aim at the identification of lead molecules inhibiting the replicative enzymes, but will not enter into the broad field of drug development.
Offers of cooperation will be made to the pharmaceutical and biotechnology industry for further drug development, on a contractual basis, and through the VIZIER Industrial Platform, which connects upfront scientific results with the pharmaceutical industry.
With no equivalent integrated programme in the world, the VIZIER project will undoubtedly have a profound impact on the field of structural genomics of emerging viruses. In particular, it is expected that VIZIER will contribute very significantly to the sequencing of new viruses (viral genomics), as well as to the deposition in the Protein Data bank of new crystal structures of viral proteins. These viral proteins can then be considered as targets for drug design.
The scientific impact on drug design is expected to be considerable through concepts and methods implemented up to the drug design step. Indeed, current drug discovery still often relies on screening compounds in a blind manner. Thousands or millions of compounds are screened on infected cells or purified enzymes, and 'hits' are selected. However, initial discovery of the inhibitor activity is followed by a lengthy and costly process of toxicology and other confirmatory studies. It is widely believed that structural biology is capable of speeding up the whole process, and providing the anticipatory power for future emerging viruses. HTP crystallography, coupled to a strong validation section such as that proposed in VIZIER, will undoubtedly reinforce this trend by leading the field. Indeed, the concept of finding a drug together with its target and the putative bottlenecks to further improvement is scientifically challenging, innovative, and promising.
VIZIER will develop new products, technologies and strategies. The products are RNA virus genomic sequences, soluble viral protein domains, their 3-D structures, assigned protein functions, and inhibitors or ligands for selected protein targets (drug leads). All the above products will have a substantial impact on the researchers' (currently limited) understanding of the RNA viral replication machinery. They will also identify entirely new targets for the development of specific drugs, with a high level of detail. Collectively, such information is seen as being of strong strategic value, not only for the health issues described, but also for the development of industrial enterprises.
Although diverse DNA-based cellular and viral parasites are also responsible for a large fraction of different human infections, none of them is so poorly controlled by drugs as the RNA viruses are. Recent viral outbreaks (H5N1, SARS, Chikungunya) confirm the difficulty of designing drugs in a timely fashion and the need for scientific anticipation. Consequently, drug development against RNA viruses - the ultimate goal of the VIZIER project - is becoming a top priority for global healthcare programmes.