Structures of initial CD4 engagement with pre-fusion, closed HIV-1 Envelope trimer and early CD4-induced conformational changes required for infection

Targeting early metastable intermediates of the SARS-CoV-2 spike for vaccine and therapeutics developmentThe ongoing global pandemic of the novel SARS-CoV-2 presents an urgent need fordevelopment of effective preventative and treatment therapies. The viral-host cell fusion (S) protein spike is aprime target for such therapies owing to its critical role in the virus lifecycle. The S protein is divided into tworegions: the N-terminal S1 domain that caps the C-terminal S2 fusion domain. Binding to host receptor via theReceptor Binding Domain (RBD) in S1 is followed by proteolytic cleavage of the spike by host proteases. Thisleads dramatic conformational transitions resulting in S1 shedding and exposure of the fusion machinery in S2,culminating in host-cell entry. Class I fusion proteins such as the CoV S protein that undergo largeconformational changes during the fusion process must, by necessity, be highly flexible and dynamic. Indeed,cryo-EM structures of the SARS-CoV-2 spike reveal considerable flexibility and dynamics in the S1 domain,especially around the RBD that exhibits two discrete conformational states - a "down" state that is shieldedfrom receptor binding, and an "up" state that is receptor-accessible. The overall goals of this study are to useour robust, high-throughput computational and experimental pipeline to define the detailed trajectory of the"down" to "up" transition of the SARS-CoV-2 S protein, identify early metastable intermediates in the fusionpathway, and exploit their structures and dynamics for identifying drug and vaccine candidates that targetSARS-CoV-2. A wealth of structural information on CoV spike proteins, including recently determined cryo-EMstructures of the SARS-CoV-2 spike, provides a rich source of detailed data from which to begin preciseexamination of macromolecular transitions underlying triggering of this fusion machine. The scientific premiseof this study is that understanding the structural dynamics and early transition kinetics of mobile regions of theSARS-CoV-2 spike will allow optimal control of vaccine and drug responses, and facilitate the development ofnovel antiviral drugs and protective vaccines. At the culmination of this study, we expect to have determinedstructures of multiple "down", "up", and intermediate states of the SARS-CoV-2 S protein. Together, thesestudies will provide important atomically detailed structural and mechanistic information for exploitation invaccine and therapeutics design.