Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein

Abstract

The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.

Role of Structural and Non-Structural Proteins and Therapeutic Targets of SARS-CoV-2 for COVID-19

“…The RBD/S1 (~200 amino acids) of S protein undergoes down-to-up conformational transition during interaction with membrane bound ACE2 recepetor, facilitating cell recognition and binding. In addition, RBD substantially contributes towards the overall mechanical stability of homotrimeric spike [14]. The S2 subunit with its fusion peptide (FP), central helix (CH), connecting domain (CD), heptad repeat (HR1/2) domain mediates integration between viral and host cell membrane.…”

TMPRSS11D and TMPRSS13 Activate the SARS-CoV-2 Spike Protein

“…While SARS-CoV-1 requires cleavage of the S protein at the S1/S2 site by host proteases in the entry steps, the S1/S2 site of the S protein of SARS-CoV-2 is cleaved by intracellular protease furin in the viral assembly step, which may affect the cell tropism and the entry efficiency of SARS-CoV-2 [ 13 ]. In addition, it is suggested that the stability and glycosylation state of the S protein regulates its conformations to maintain the contact with ACE2 receptor, which is also related to vital entry efficiency [ 14 , 15 , 16 ].…”

The Combination of Bromelain and Acetylcysteine (BromAc) Synergistically Inactivates SARS-CoV-2

“…[ 20 , 23 , 24 , 25 , 26 , 27 ]. More recently, Acetylcysteine has been used in the development of therapies for respiratory infections such as influenza and COVID-19 [ 28 , 29 , 30 ], where the integrity of the spike protein is vital for infection [ 12 , 13 ]. A hypothesized mechanism of action could be the unfolding of the spike glycoprotein and the reduction of its disulfide bonds.…”

“…The entry of viruses into mammalian cells, or “virus internalization”, is a key mechanism of enveloped virus infection and is based on dynamic conformational changes of their surface glycoproteins, namely, as mediated by disulfide bond reduction and regulated by cell surface oxydoreductases and proteases [ 5 , 8 , 9 , 10 , 11 ]. SARS-CoV-2 entry into host cells has been shown to start with destabilization of the spike protein through allosteric mechanical transition, which induces a conformational change from the closed “down” state to open “up” state of the receptor binding domain (RBD) of the spike protein [ 12 , 13 ]. The conformational changes of RBD and virus binding are induced by TMPRSS2 or Cathepsin L, which trigger the transition from the pre-fusion to post-fusion state [ 5 , 12 , 13 ].…”

“…SARS-CoV-2 entry into host cells has been shown to start with destabilization of the spike protein through allosteric mechanical transition, which induces a conformational change from the closed “down” state to open “up” state of the receptor binding domain (RBD) of the spike protein [ 12 , 13 ]. The conformational changes of RBD and virus binding are induced by TMPRSS2 or Cathepsin L, which trigger the transition from the pre-fusion to post-fusion state [ 5 , 12 , 13 ]. The energy liberated by disulfide bond reduction increases protein flexibility, which is maximal when the reduced state is complete [ 8 ], thus allowing the fusion of host–virus membranes, which is otherwise impossible due to the repulsive hydration forces present before reduction [ 5 ].…”