Allostery for Medicine
Allostery is the basis of all cellular signaling processes. Molecular mechanisms of allostery are key to understanding the fundamentals of cellular functions and for biomedical applications. In particular, the link between allostery and catalysis in biological systems is highly relevant for the development of new drugs and biotechnology. We studied allostery in a number of vital cellular processes such as translation, nitric oxide cellular signaling, cellular motility, carbohydrate metabolism, and innate immunity. The results of these studies opened new ways to overcome antibiotic resistance and to develop new neuroprotective drugs, anti-parasitic treatments, and treatments against myosin-related diseases.
In the works on the allostery and catalysis of the ribosome we studied structures and mechanisms of ribosomal components involved in the assembly of the central protuberance and interactions with the P-site tRNA, 5S and 23S rRNAs, formation and dynamics of side protuberance and interactions with mRNA, formation of the polypeptide exit tunnel adjacent to the catalytic PT center and erythromycin resistance, regulation of the peptidyltransferase activity, and delivery of initiator tRNA to the small subunit. The interaction mechanisms and conformational dynamics of ribosomal proteins L1, L4, L5, L18, L22, L30 (marked yellow), 5S RNA fragments, initiation factor IF2 and charged initiator tRNA, which are essential for ribosome assembly and catalytic function, were revealed. These data contributed to an understanding of the translation mechanism (see the background information for the Nobel Prize in Chemistry 2009) and were used in several patents on the methods of rational design of antibiotics.
In the series of works on the mechanisms of allosteric regulation of NO synthesis by NOS isoforms, we identified the most promising determinants for isoform-selective inhibition of these enzymes. These elements, including the substrate access channel, the “back wall” of the heme cavity, and the binding site of the H4B cofactor, are involved in allosteric regulation of enzymatic activity and offer new ways to develop isoform-selective NOS inhibitors. The properties of these allosteric sites were studied, and the isoform-selective inhibitor scaffolds targeting each site were formulated and tested. The results of these studies contributed to the development of neuroprotective drugs.
The works on the allosteric regulation of myosin-2 motor activity revealed novel links between the allostery of the myosin motor domain and its catalytic activity. In particular, the pentabromopseudilin (PBP) allosteric site and the relay pathway, connecting this site with the catalytic center of the myosin-2 motor domain, were discovered. The PBP allosteric site can be used to develop specific allosteric inhibitors of myosin isoforms with a wide range of potential therapeutic applications in the treatment of diseases, including cancer, heart failure, and malaria.
Allosteric mechanisms underlying the enzymatic cycle and catalysis of human and pathogenic UGP were identified. For the octameric human UGP, we demonstrated that oligomerization plays a number of important functional roles that help hUGP to fulfill its function as an exclusive switch in human carbohydrate metabolism. In pathogen Leishmania major UGP (LmUGP) generates the NDP-pools for glycocalyx formation, which is essential for infectivity. In our work, we discovered a previously unknown specific allosteric inhibition site in LmUGP and developed an allosteric inhibitor targeting this site. This work laid the foundation for the development of new antileishmanial therapies.
The innate immune sensors activate interferon-driven antiviral responses upon recognition of PAMPs and serve as a rheostat for the metabolic activity of the microbiota and its exposure to diet, xenobiotics, and infections. The ability to modulate innate immune sensors opens new ways to novel anti-viral and anti-inflammatory drugs, and therapies against cancer and many aging-associated metabolic, neoplastic, autoimmune or autoinflammatory disorders. In our work, we studied the link between allostery and catalysis for 2’-5’-oligoadenylate synthetase and cyclic GMP-AMP synthase – the innate immune sensors that trigger RNase L and STING pathways in response to infections. We showed that OAS activation involves a sequential allosteric mechanism, defined the individual roles of dsRNA and substrates in OAS activation, and discovered the mechanisms of the 2’-specificity of OAS product formation and functional differentiation between OAS and cGAS. The new data obtained in this study and the detailed analysis of the activation mechanisms of the OAS1/cGAS family provided new fundamental insights into the function of these key innate immune sensors and laid a foundation for rational design of novel immunotherapeutic agents.