#stapled binding

Stapled binding free#

(c) The structures and sequences of the truncated α1 and five modified peptides. (b) ACE2 interacts with amino acids of RBD (white ribbon) through its α1 helix (green ribbon). Out of three spike proteins, two (blue and red surface) have their RBD buried (RBD down) and one (white surface) is with an exposed RBD (RBD up) conformation which binds at one end of human ACE2 (light green cartoon). (a) The trimeric assembly of SARS-CoV-2 spike protein in complex with human ACE2 protein. Unlike the other targets, the protein–protein interaction interface between ACE2 and RBD is quite extended and flexible, thereby designing an inhibitor is challenging. Among these, RBD has been targeted most of the time because of its direct interaction with the human ACE2 receptor. The continuous effort to design suitable inhibitor molecules, which can be, used as drugs to target different proteins of the virus, for example, the main protease (MP), non-structural proteins (NSP) domains, receptor-binding domain (RBD), etc. The attempts made to find the cure for this includes designing vaccines, antibodies, and drugs that can inhibit the crucial stages of the infection process. The complexation eventually leads to the internalization of the virus and host membrane and the subsequent transfer of viral genetic material into the host cell. A closer look at the RBD-ACE2 complex shows that the complexation is guided by the interaction of the α1 helix of ACE2 with the surface residues of the RBD. During the virus attachment stage, the receptor binding domain (RBD) of one monomer gets activated and attaches to the human ACE2 receptor followed by membrane fusion and internalization of genetic material. The spike protein has a trimeric structure and each monomer is formed by several structural domains (Figure 1a). In the very first step, the Spike protein of SARS-CoV-2 binds to the human ACE2 receptor. The process of viral infection comprises several stages and different components of the virus are involved in these stages. In addition to that, several new variants of the virus have evolved which can escape the binding of antibodies, effective against the native form of the virus. the mutations have made the virus more resistant to neutralizing antibodies. Although SARS-CoV-2 belongs to the same coronavirus family as MERS-CoV, SARS-CoV, etc. are caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and these are highly contagious in nature. Several respiratory syndromes, pneumonia, etc. The global pandemic caused by COVID-19 has been the cause of more than 5.5 million deaths as of January 2022 and has massively affected the global economy. The understanding of the relation of the nature of the stapling agent with their binding affinity opens up the avenue to explore stapled peptides as therapeutic against SARS-CoV-2.

Stapled binding free#

Analyses of the mechanistic detail reveal that a reorganization of amino acids at the RBD-ACE2 interface produces favorable enthalpy of binding whereas conformational restriction of the free peptide reduces the loss in entropy to result higher binding affinity. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD-ACE2 binding. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. The α1 helix of ACE2, which forms direct contact with the RBD surface, has been used as a template in the current study to design stapled peptide therapeutics. Therefore, the RBD of SARS-CoV-2 can be used as a target to design therapeutics. The gateway of the virus to the host cell is mediated by the binding of the receptor binding domain (RBD) of the virus spike protein to the angiotensin-converting enzyme 2 (ACE2) of the human cell. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic-based treatment for COVID-19. Despite the development and administration of different vaccines, the situation is still worrisome as the virus is constantly mutating to produce newer variants some of which are highly infectious. Since its first detection in 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has been the cause of millions of deaths worldwide.