Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective.

BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. METHODS: In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. CONCLUSION: Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.

Unravelling viral dynamics through molecular dynamics simulations - A brief overview.

Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A virus structure is metastable and highly responsive to environmental changes. Although major events of a virus life cycle are well characterized, several important questions with respect to how the nucleocapsid assemble/disassemble remain to be explored. In recent years due to enhanced computational power, molecular dynamics (MD) simulations have become an attractive alternative for addressing these questions since it is challenging to probe dynamic behavior with in vitro experimentation. The ability to simulate a complete virus particle provides an unprecedented atomic level resolution which can be used to understand its behavior under specific conditions. The current review outlines contributions made by all-atom and coarse-grained MD simulations towards understanding the mechanics and dynamics of virus structure and function. Databases and programs which facilitate such in silico investigations have also been discussed.

Interaction of Nanomaterials with Protein-Peptide.

Nanomaterials have undergone rapid development in the last few decades, galvanized by the versatility of their functional attributes and many inherent advantages over bulk materials. The state of art experimental techniques to synthesize nanoparticles (NPs) from varied sources offers unprecedented opportunities for utilization and exploration of multifaceted biological activities. Such formulations demand a preliminary understanding of the interaction between NPs and biomolecules. Most of these interactions depend on the external morphology of the NPs, like the shape, size, charge and surface chemistry. In addition, most experimental techniques are limited to cellular-level data, without the atomistic details of mechanisms that lead to these interactions. Consequently, recent studies have determined these atomistic events through in-silico techniques, which provide a better understanding and integrative details of interactions between biomolecules and different NPs. Therefore, while delineating the protein-NPs interaction, it is imperative to define the consequences of nanomaterial's introduction and derive data for the formulation of better therapeutic interventions. This review briefly discusses varied types of NPs, their potential applications and interactions with peptides and proteins.

In silico analysis of antiviral phytochemicals efficacy against Epstein-Barr virus glycoprotein H.

Epstein-Barr virus is a tumor-associated, enveloped virus with glycoprotein receptor gHgL on its surface. gH attaches to epithelial or B cells and mediates internalization. Till date, no specific anti-EBV FDA approved drug is available. Targeting gH may aid in designing virus-specific therapeutics and reducing the drug induced complications in host. We investigated the influence of antiviral phytochemicals on gH using computational approaches. Through molecular docking, we performed binding energy analysis of cellocidin, bruceantin, EGCG, formononetin and sesquiterpene lactones with gH DII/DIII interface, crucial for gH functions. Further, to cause any perturbations in the protein function, the molecules must bind stably to gH. Bruceantin and EGCG interacted with high affinities to gH. Simulation of these two molecules revealed stable binding with gH throughout 100 ns moreover, van der Waal interactions stabilized overall binding. Mutation of amino acids like V265, L269, L315, I423, I459, L474 and F475 involved in stable binding to gH was predicted deleterious to protein function. We obtained no difference in RMSD between these two ligands and minor deviations in the RMSF were noticed compared to gH. Conclusively, our study provided insights into the potential of bruceantin and EGCG to target gH. Different amino acids are involved in binding of each ligand to gH, engagement of certain amino acids may affect the virus binding with epithelial or B cells. The interaction of the ligand with gH may trap it in its native conformation or induce structural flexibility thereby inhibiting the interaction with host receptors or other glycoproteins.Communicated by Ramaswamy H. Sarma.

Exploring the interaction of bioactive kaempferol with serum albumin, lysozyme and hemoglobin: A biophysical investigation using multi-spectroscopic, docking and molecular dynamics simulation studies.

In recent years research based on kaempferol (KMP) has shown its potential therapeutic applications in medicinal chemistry and clinical biology. Therefore, to understand its molecular recognition mechanism, we studied its interactions with the carrier proteins, namely, human serum albumin (HSA), bovine hemoglobin (BHb) and hen egg white lysozyme (HEWL). The ligand, KMP was able to quench the intrinsic fluorescence of these three proteins efficiently through static quenching mode. The binding constant (Kb) for the interactions of KMP with these three proteins were found in the following order: HSA-KMP > BHb-KMP > HEWL-KMP. Different non-covalent forces such as hydrogen bonding and hydrophobic forces played a major role in the binding of KMP with HSA and HEWL, whereas hydrogen bonding and van der Waals forces contribute to the complexation of BHb with KMP. KMP was able to alter the micro-environment near the Trp fluorophore of the proteins. KMP altered the secondary structural component of all three proteins. The putative binding sites and the residues surrounding the KMP molecule within the respective protein matrix were determined through molecular docking and molecular dynamics (MD) simulation studies. The conformational flexibility of the ligand KMP and the three individual proteins were also evident from the MD simulation studies.

Computational Analysis of the Silver Nanoparticle-Human Serum Albumin Complex.

Drug delivery in excess concentrations and at not-specified sites inside the human body adversely affects the body and gives rise to other diseases. Several methods have been developed to deliver the drugs in required amounts and at specific targets. Nanoparticle-mediated drug delivery is one such approach and has gained success at primary levels. The effect of nanoparticles on the human body needs important apprehension, and it has been unraveled by assessing the protein-nanoparticle interactions. Here, we have measured the impact of silver nanoparticles (AgNPs) on the human serum albumin (HSA) structure and function with the help of all-atom molecular dynamics simulations (MDS). HSA is a transport protein, and any change in the structure may obstruct its function. The post MD analyses showed that the NP interacts with HSA and the conjugated system got stabilized with time evolution of trajectories. The present investigation confirms that the AgNP interacts with HSA without affecting its tertiary and secondary structures and in turn the protein function as well. AgNP application is recommended in transporting conjugated drug molecules as it has no adverse effect on serum proteins. Since HSA is present in the circulatory system, it may open various applications of AgNPs in the biomedical field.

Targeting the heme protein hemoglobin by (-)-epigallocatechin gallate and the study of polyphenol-protein association using multi-spectroscopic and computational methods.

In this work, the interaction of a bioactive tea polyphenol (-)-epigallocatechin gallate (EGCG) with bovine hemoglobin (BHb) along with its anti-oxidative behavior and the anti-glycation property have been explored using multi-spectroscopic and computational techniques. The binding affinity for EGCG towards BHb was observed to be moderate in nature with an order of 104 M-1, and the fluorescence quenching mechanism was characterized by an unusual static quenching mechanism. The binding constant (Kb) showed a continuous enhancement with temperature from 3.468 ± 0.380 × 104 M-1 at 288 K to 6.017 ± 0.601 × 104 M-1 at 310 K. The fluorescence emission measurements along with molecular docking studies indicated that EGCG binds near the most dominant fluorophore of BHb (ß2-Trp37, at the interface of α1 and ß2 chains) within the pocket formed by the α1, α2 and ß2 chains. The sign and magnitude of the thermodynamic parameters, changes in enthalpy (ΔH = +17.004 ± 1.007 kJ mol-1) and in entropy (ΔS = +146.213 ± 2.390 J K-1 mol-1), indicate that hydrophobic forces play a major role in stabilizing the BHb-EGCG complex. The micro-environment around the EGCG binding site showed an increase in hydrophobicity upon ligand binding. The binding of EGCG with BHb leads to a decrease in the α-helical content, whereas that of the ß-sheet increased. FTIR studies also indicated that the secondary structure of BHb changed upon binding with EGCG, along with providing further support for the presence of hydrophobic forces in the complexation process. Molecular docking studies indicated that EGCG binds within the cavity of α1, α2, and ß2 chains surrounded by residues such as α1- Lys99, α1-Thr134, α1-Thr137, α1-Tyr140, α2-Lys127 and ß2-Trp37. Molecular dynamics simulation studies indicated that EGCG conferred additional stability to BHb. Furthermore, moving away from the binding studies, EGCG was found to prevent the glyoxal (GO)-mediated glycation process of BHb, and it was also found to act as a potent antioxidant against the photo-oxidative damage of BHb.

Insulin adsorption onto zinc oxide nanoparticle mediates conformational rearrangement into amyloid-prone structure with enhanced cytotoxic propensity.

BACKGROUND: Injection localized amyloidosis is one of the most prevalent disorders in type II diabetes mellitus (TIIDM) patients relying on insulin injections. Previous studies have reported that nanoparticles can play a role in the amyloidogenic process of proteins. Hence, the present study deals with the effect of zinc oxide nanoparticles (ZnONP) on the amyloidogenicity and cytotoxicity of insulin. METHODS: ZnONP is synthesised and characterized using XRD, Zeta Sizer, UV-Visible spectroscope and TEM. The characterization is followed by ZnONP interaction with insulin, which is studied employing fluorescence spectroscopes, isothermal titration calorimetry and molecular dynamics simulations. The interaction leads insulin conformational rearrangement into amyloid-like fibril, which is studied using thioflavin T dye binding assay, circular dichroism spectroscopy and TEM, followed by cytotoxicity propensity using Alamar Blue dye reduction assay. RESULTS: Insulin has very weak interaction with ZnONP interface. Insulin at studied concentration forms amorphous aggregates at physiological pH, whereas in presence of ZnONP interface amyloid-like fibrils are formed. While the amyloid-like fibrils are cytotoxic to MIN6 and THP-1 cell lines, insulin and ZnONP individual solutions and their fresh mixtures enhance the cells proliferation. CONCLUSIONS: The presence of ZnONP interface enhances insulin fibrillation at physiological pH by providing a favourable template for the nucleation and growth of insulin amyloids. GENERAL SIGNIFICANCE: The studied protein-nanoparticle system from protein conformational dynamics point of view throws caution over nanoparticle use in biological applications, especially in vivo applications, considering the amyloidosis a very slow but non-curable degenerative disease.