New theoretic and experimental approaches to drug discovery. Environmental, demographic and ecological reasons suggest that either novel or known viruses will continue to emerge worldwide, posing new threats to the human population. Additionally, therapeutic interventions present different outcomes; for example, vaccination campaigns in the Third World often encounter local distribution problems and reach an insufficient fraction of the population. For many viruses no vaccine is available, such that the toll death is high, particularly in tropical countries and among infants. On the other hand, resistance of bacteria to know antibiotics is increasingly a serious threat, often associated to nosocomial infections. As a result, new ideas and approaches to the discovery or design of new effective drugs are a high priority in all civilized countries, to prevent and be ready to face potential pandemics. In this context, our group at the University of Milano, in collaboration with several European and extra- European labs, has been exploring the structural and functional properties of enzymes involved in the replication of (+)stranded RNA viruses as targets for the design of antiviral drugs. The rationale behind the choice of specific target viral is the idea that these are structurally and functionally sufficiently different from their human counterparts; thus, blocking the virus enzyme with a new drug should not be reflected by adverse reactions in the human host. The discovery approach applied in our laboratory has been based on a series of specific experimental steps: i) the analysis of crystal structure of the free enzymes, through X-ray crystallography; ii) in silico (computational) preliminary screening of selected enzyme regions towards which the drug search is targeted (e.g. mostly the enzyme active sites); iii) biochemical and biophysical tests of enzyme inhibition; iv) crystal structure analyses of enzyme/inhibitor complexes; v) in cell/in vivo testing; vi) inference for drug-lead optimization. This research method proved effective in discovering low molecular weight inhibitors of two key enzymes from Yellow fever virus (and partly for Dengue virus), and for Norovirus. Specifically, we targeted Norovirus studying the long known drug Suramin (used in the therapy of ‘sleeping sickness’), which was selected through the procedure described above through our in silico docking screenings. Our crystallographic and inhibition assays allowed to highlight the inhibitor binding mode and satisfactory functional inhibitory parameters. Subsequently, in the context of an international collaboration, we could test a series of Suramin molecular fragments, in search of new active compounds endowed with suitable pharmacological parameters. The described research activity, which is based on new conceptual and multidisciplinary approaches to drug discovery, has led to the production of several small molecules that will be further developed into antiviral compounds.
PoreMatMod.jl: Julia Package for in Silico Postsynthetic Modification of Crystal Structure Models
