Molecular Dynamics Simulation Study of the Interaction between Human Angiotensin Converting Enzyme 2 and Spike Protein Receptor Binding Domain of the SARS-CoV-2 B.1.617 Variant

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has had a significant impact on people’s daily lives. The rapidly spreading B.1.617 lineage harbors two key mutations—L452R and E484Q—in the receptor binding domain (RBD) of its spike (S) protein. To understand the impact and structural dynamics of the variations in the interface of S protein and its host factor, the human angiotensin-converting enzyme 2 (hACE2), triplicate 500 ns molecular dynamics simulations were performed using single (E484Q or L452R) and double (E484Q + L452R) mutant structures and compared to wild type simulations. Our results indicate that the E484Q mutation disrupts the conserved salt bridge formed between Lys31 of hACE2 and Glu484 of S protein. Additionally, E484Q, which could favor the up conformation of the RBD, may help in enhanced hACE2 binding and immune escape. L452R introduces a charged patch near the binding surface that permits increased electrostatic attraction between the proteins. An improved network of intramolecular interactions observed is likely to increase the stability of the S protein and conformational changes may prevent the binding of neutralizing antibodies. The results obtained from the molecular dynamics simulations suggest that structural and dynamic changes introduced by these variations enhance the affinity of the viral S protein to hACE2 and could form the basis for further studies.

Download Full-text

Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.1c06050 ◽

2021 ◽

Author(s):

Solène Lecot ◽

Yann Chevolot ◽

Magali Phaner-Goutorbe ◽

Christelle Yeromonahos

Keyword(s):

Molecular Dynamics ◽

Binding Energy ◽

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Spike Protein ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Energy Increase ◽

Angiotensin Converting Enzyme 2 ◽

Dynamics Simulations

Download Full-text

The biomaterial polyphosphate blocks stoichiometric binding of the SARS-CoV-2 S-protein to the cellular ACE2 receptor

Biomaterials Science ◽

10.1039/d0bm01244k ◽

2020 ◽

Vol 8 (23) ◽

pp. 6603-6610 ◽

Cited By ~ 1

Author(s):

Werner E. G. Müller ◽

Meik Neufurth ◽

Hadrian Schepler ◽

Shunfeng Wang ◽

Emad Tolba ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Blood Platelets ◽

Binding Domain ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Low Concentrations

The polymer polyphosphate, abundant in blood platelets, blocks the binding of the receptor-binding domain (RBD) of the SARS- spike (S)-protein to the angiotensin-converting enzyme 2 (ACE2) at low concentrations.

Download Full-text

Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation

10.26434/chemrxiv.14135138.v1 ◽

2021 ◽

Author(s):

Kazuki Watanabe ◽

Chiduru Watanabe ◽

Teruki Honma ◽

Yu-Shi Tian ◽

Yusuke Kawashima ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Interaction Energy ◽

Intermolecular Interaction ◽

Molecular Orbital ◽

Receptor Binding ◽

Binding Domain ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

S Protein ◽

Angiotensin Converting Enzyme 2

The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2 (hACE2). The receptor-binding domain (RBD) of the S-protein has been considered critical for this interaction and acts as the target of numerous neutralizing antibodies and antiviral peptides. This study used the fragment molecular orbital (FMO) method to analyze the interactions between RBD and antibodies/peptides and extracted crucial residues that can be used to epitopes. The interactions evaluated as inter-fragment interaction energy (IFIE) values between the RBD and 12 antibodies/peptides showed a fairly good correlation with the experimental activity pIC50 (R2 = 0.540). Nine residues (T415, K417, Y421, F456, A475, F486, N487, N501, and Y505) were confirmed as crucial. Pair interaction energy decomposition analyses (PIEDA) showed that hydrogen bonds, electrostatic interactions, and π-orbital interactions are important. Our results provide essential information for understanding SARS-CoV-2-antibodies/peptide binding and may play roles in future antibody/antiviral drug design.

Download Full-text

Intermolecular Interaction Analyses on SARS-CoV-2 Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/peptide Using Fragment Molecular Orbital Calculation

10.26434/chemrxiv.14135138 ◽

2021 ◽

Author(s):

Kazuki Watanabe ◽

Chiduru Watanabe ◽

Teruki Honma ◽

Yu-Shi Tian ◽

Yusuke Kawashima ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Interaction Energy ◽

Intermolecular Interaction ◽

Molecular Orbital ◽

Receptor Binding ◽

Binding Domain ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

S Protein ◽

Angiotensin Converting Enzyme 2

Download Full-text

ACE2 fragment as a decoy for novel SARS-Cov-2 virus

10.1101/2020.04.06.028647 ◽

2020 ◽

Cited By ~ 1

Author(s):

Fabiana Renzi ◽

Dario Ghersi

Keyword(s):

Molecular Dynamics ◽

Angiotensin Converting Enzyme ◽

Molecular Dynamics Simulations ◽

Cellular Membrane ◽

Converting Enzyme ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Viral Binding ◽

Binding Surface ◽

Dynamics Simulations

Novel SARS-Cov-2 enters human cells via interaction between the surface spike (S) glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the S protein to ACE2, docking experiments, and molecular dynamics simulations we computationally identified a minimal, stable fragment of ACE2. This fragment binds to the S protein, is soluble, and appears not to bind to the physiological ligand angiotensinII. These results suggest a possible use of the ACE2 fragment as a decoy that could interfere with viral binding by competition.

Download Full-text

Competitive SARS-CoV-2 Serology Reveals Most Antibodies Targeting the Spike Receptor-Binding Domain Compete for ACE2 Binding

mSphere ◽

10.1128/msphere.00802-20 ◽

2020 ◽

Vol 5 (5) ◽

Cited By ~ 3

Author(s):

James R. Byrnes ◽

Xin X. Zhou ◽

Irene Lui ◽

Susanna K. Elledge ◽

Jeff E. Glasgow ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Viral Entry ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Block Interaction ◽

Angiotensin Converting Enzyme 2 ◽

Protein Receptor

ABSTRACT As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread around the world, there is an urgent need for new assay formats to characterize the humoral response to infection. Here, we present an efficient, competitive serological assay that can simultaneously determine an individual’s seroreactivity against the SARS-CoV-2 Spike protein and determine the proportion of anti-Spike antibodies that block interaction with the human angiotensin-converting enzyme 2 (ACE2) required for viral entry. In this approach based on the use of enzyme-linked immunosorbent assays (ELISA), we present natively folded viral Spike protein receptor-binding domain (RBD)-containing antigens via avidin-biotin interactions. Sera are then competed with soluble ACE2-Fc, or with a higher-affinity variant thereof, to determine the proportion of ACE2 blocking anti-RBD antibodies. Assessment of sera from 144 SARS-CoV-2 patients ultimately revealed that a remarkably consistent and high proportion of antibodies in the anti-RBD pool targeted the epitope responsible for ACE2 engagement (83% ± 11%; 50% to 107% signal inhibition in our largest cohort), further underscoring the importance of tailoring vaccines to promote the development of such antibodies. IMPORTANCE With the emergence and continued spread of the SARS-CoV-2 virus, and of the associated disease, coronavirus disease 2019 (COVID-19), there is an urgent need for improved understanding of how the body mounts an immune response to the virus. Here, we developed a competitive SARS-CoV-2 serological assay that can simultaneously determine whether an individual has developed antibodies against the SARS-CoV-2 Spike protein receptor-binding domain (RBD) and measure the proportion of these antibodies that block interaction with the human angiotensin-converting enzyme 2 (ACE2) required for viral entry. Using this assay and 144 SARS-CoV-2 patient serum samples, we found that a majority of anti-RBD antibodies compete for ACE2 binding. These results not only highlight the need to design vaccines to generate such blocking antibodies but also demonstrate the utility of this assay to rapidly screen patient sera for potentially neutralizing antibodies.

Download Full-text

LL-37 fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro

10.1101/2020.12.02.408153 ◽

2020 ◽

Author(s):

Annika Roth ◽

Steffen Lütke ◽

Denise Meinberger ◽

Gabriele Hermes ◽

Gerhard Sengle ◽

...

Keyword(s):

Vitamin D ◽

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Viral Entry ◽

Binding Domain ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Cell Infection ◽

S Protein

AbstractObjectiveSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen accountable for the coronavirus disease 2019 (COVID-19) pandemic. Viral entry via binding of the receptor binding domain (RBD) located within the S1 subunit of the SARS-CoV-2 Spike (S) protein to its target receptor angiotensin converting enzyme (ACE) 2 is a key step in cell infection. The efficient transition of the virus is linked to a unique protein called open reading frame (ORF) 8. As SARS-CoV-2 infections can develop into life-threatening lower respiratory syndromes, effective therapy options are urgently needed. Several publications propose vitamin D treatment, although its mode of action against COVID-19 is not fully elucidated. It is speculated that vitamin D’s beneficial effects are mediated by up-regulating LL-37, a well-known antimicrobial peptide with antiviral effects.MethodsRecombinantly expressed SARS-CoV-2 S protein, the extended S1 subunit (S1e), the S2 subunit (S2), the receptor binding domain (RBD), and ORF8 were used for surface plasmon resonance (SPR) studies to investigate LL-37’s ability to bind to SARS-CoV-2 proteins and to localize its binding site within the S protein. Binding competition studies were conducted to confirm an inhibitory action of LL-37 on the attachment of SARS-CoV-2 S protein to its entry receptor ACE2.ResultsWe could show that LL-37 binds to SARS-CoV-2 S protein (LL-37/SStrep KD = 410 nM, LL-37/SHis KD = 410 nM) with the same affinity, as SARS-CoV-2 binds to hACE2 (hACE2/SStrep KD = 370 nM, hACE2/SHis KD = 370 nM). The binding is not restricted to the RBD of the S protein, but rather distributed along the entire length of the protein. Interaction between LL-37 and ORF8 was detected with a KD of 290 nM. Further, inhibition of the binding of SStrep (IC50 = 740 nM), S1e (IC50 = 170 nM), and RBD (IC50 = 130 nM) to hACE2 by LL-37 was demonstrated.ConclusionsWe have revealed a biochemical link between vitamin D, LL-37, and COVID-19 severity. SPR analysis demonstrated that LL-37 binds to SARS-CoV-2 S protein and inhibits binding to its receptor hACE2, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. Further, our results provide evidence that the direct use of LL-37 by inhalation and systemic application may reduce the severity of COVID-19.

Download Full-text

A Drug Repurposing Approach for Antimalarials Interfering with SARS-CoV-2 Spike Protein Receptor Binding Domain (RBD) and Human Angiotensin-Converting Enzyme 2 (ACE2)

Pharmaceuticals ◽

10.3390/ph14100954 ◽

2021 ◽

Vol 14 (10) ◽

pp. 954

Author(s):

Paolo Coghi ◽

Li Jun Yang ◽

Jerome P. L. Ng ◽

Richard K. Haynes ◽

Maurizio Memo ◽

...

Keyword(s):

Angiotensin Converting Enzyme ◽

Receptor Binding ◽

Cell Invasion ◽

Binding Domain ◽

Spike Protein ◽

Interaction Patterns ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Angiotensin Converting Enzyme 2

Host cell invasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is mediated by the interaction of the viral spike protein (S) with human angiotensin-converting enzyme 2 (ACE2) through the receptor-binding domain (RBD). In this work, computational and experimental techniques were combined to screen antimalarial compounds from different chemical classes, with the aim of identifying small molecules interfering with the RBD-ACE2 interaction and, consequently, with cell invasion. Docking studies showed that the compounds interfere with the same region of the RBD, but different interaction patterns were noted for ACE2. Virtual screening indicated pyronaridine as the most promising RBD and ACE2 ligand, and molecular dynamics simulations confirmed the stability of the predicted complex with the RBD. Bio-layer interferometry showed that artemisone and methylene blue have a strong binding affinity for RBD (KD = 0.363 and 0.226 μM). Pyronaridine also binds RBD and ACE2 in vitro (KD = 56.8 and 51.3 μM). Overall, these three compounds inhibit the binding of RBD to ACE2 in the μM range, supporting the in silico data.

Download Full-text

The flexibility of ACE2 in the context of SARS-CoV-2 infection

10.1101/2020.09.16.300459 ◽

2020 ◽

Cited By ~ 3

Author(s):

E. P. Barros ◽

L. Casalino ◽

Z. Gaieb ◽

A. C. Dommer ◽

Y. Wang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Receptor Binding ◽

Rational Design ◽

Binding Domain ◽

Full Length ◽

Receptor Binding Domain ◽

Spike Glycoprotein ◽

Linker Region ◽

Dynamics Simulations

AbstractThe COVID-19 pandemic has swept over the world in the past months, causing significant loss of life and consequences to human health. Although numerous drug and vaccine developments efforts are underway, many questions remain outstanding on the mechanism of SARS-CoV-2 viral association to angiotensin-converting enzyme 2 (ACE2), its main host receptor, and entry in the cell. Structural and biophysical studies indicate some degree of flexibility in the viral extracellular Spike glycoprotein and at the receptor binding domain-receptor interface, suggesting a role in infection. Here, we perform all-atom molecular dynamics simulations of the glycosylated, full-length membrane-bound ACE2 receptor, in both an apo and spike receptor binding domain (RBD) bound state, in order to probe the intrinsic dynamics of the ACE2 receptor in the context of the cell surface. A large degree of fluctuation in the full length structure is observed, indicating hinge bending motions at the linker region connecting the head to the transmembrane helix, while still not disrupting the ACE2 homodimer or ACE2-RBD interfaces. This flexibility translates into an ensemble of ACE2 homodimer conformations that could sterically accommodate binding of the spike trimer to more than one ACE2 homodimer, and suggests a mechanical contribution of the host receptor towards the large spike conformational changes required for cell fusion. This work presents further structural and functional insights into the role of ACE2 in viral infection that can be exploited for the rational design of effective SARS-CoV-2 therapeutics.Statement of SignificanceAs the host receptor of SARS-CoV-2, ACE2 has been the subject of extensive structural and antibody design efforts in aims to curtail COVID-19 spread. Here, we perform molecular dynamics simulations of the homodimer ACE2 full-length structure to study the dynamics of this protein in the context of the cellular membrane. The simulations evidence exceptional plasticity in the protein structure due to flexible hinge motions in the head-transmembrane domain linker region and helix mobility in the membrane, resulting in a varied ensemble of conformations distinct from the experimental structures. Our findings suggest a dynamical contribution of ACE2 to the spike glycoprotein shedding required for infection, and contribute to the question of stoichiometry of the Spike-ACE2 complex.

Download Full-text

Computational analysis on the ACE2-derived peptides for neutralizing the ACE2 binding to the spike protein of SARS-CoV-2

10.1101/2020.05.03.075473 ◽

2020 ◽

Author(s):

Cecylia S. Lupala ◽

Vikash Kumar ◽

Xuanxuan Li ◽

Xiao-dong Su ◽

Haiguang Liu

Keyword(s):

Molecular Dynamics ◽

Severe Acute Respiratory Syndrome ◽

Angiotensin Converting Enzyme ◽

Computational Analysis ◽

Spike Protein ◽

Short Peptides ◽

Receptor Binding Domain ◽

Converting Enzyme ◽

Angiotensin Converting Enzyme 2 ◽

Dynamics Simulations

ABSTRACTThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19, is spreading globally and has infected more than 3 million people. It has been discovered that SARS-CoV-2 initiates the entry into cells by binding to human angiotensin-converting enzyme 2 (hACE2) through the receptor binding domain (RBD) of its spike glycoprotein. Hence, drugs that can interfere the SARS-CoV-2-RBD binding to hACE2 potentially can inhibit SARS-CoV-2 from entering human cells. Here, based on the N-terminal helix α1 of human ACE2, we designed nine short peptides that have potential to inhibit SARS-CoV-2 binding. Molecular dynamics simulations of peptides in the their free and SARS-CoV-2 RBD-bound forms allow us to identify fragments that are stable in water and have strong binding affinity to the SARS-CoV-2 spike proteins. The important interactions between peptides and RBD are highlighted to provide guidance for the design of peptidomimetics against the SARS-CoV-2.

Download Full-text