Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory.

The spike protein (S-protein) is a crucial part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with its many domains responsible for binding, fusion, and host cell entry. In this review we use the density functional theory (DFT) calculations to analyze the atomic-scale interactions and investigate the consequences of mutations in S-protein domains. We specifically describe the key amino acids and functions of each domain, which are essential for structural stability as well as recognition and fusion processes with the host cell; in addition, we speculate on how mutations affect these properties. Such unprecedented large-scale ab initio calculations, with up to 5000 atoms in the system, are based on the novel concept of amino acid-amino acid-bond pair unit (AABPU) that allows for an alternative description of proteins, providing valuable information on partial charge, interatomic bonding and hydrogen bond (HB) formation. In general, our results show that the S-protein mutations for different variants foster an increased positive partial charge, alter the interatomic interactions, and disrupt the HB networks. We conclude by outlining a roadmap for future computational research of biomolecular virus-related systems.

Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein.

The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid-amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2' cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex.

The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present, in more conspicuous atomic level detail, the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.

Binding Interactions between Receptor-Binding Domain of Spike Protein and Human Angiotensin Converting Enzyme-2 in Omicron Variant.

The emergence of new SARS-CoV-2 Omicron variant of concern (OV) has exacerbated the COVID-19 pandemic because of a large number of mutations in the spike protein, particularly in the receptor-binding domain (RBD), resulting in highly contagious and/or vaccine-resistant strains. Herein, we present a systematic analysis based on detailed molecular dynamics (MD) simulations in order to understand how the OV RBD mutations affect the ACE2 binding. We show that the OV RBD binds to ACE2 more efficiently and tightly predominantly because of strong electrostatic interactions, thereby promoting increased infectivity and transmissibility compared to other strains. Some of the OV RBD mutations are predicted to affect the antibody neutralization either through their role in the S-protein conformational changes, such as S371L, S373P, and S375F, or through changing its surface charge distribution, such as G339D, N440K, T478K, and E484A. Other mutations, such as K417N, G446S, and Y505H, decrease the ACE2 binding, whereas S447N, Q493R, G496S, Q498R, and N501Y tend to increase it.

Delta Variant with P681R Critical Mutation Revealed by Ultra-Large Atomic-Scale Ab Initio Simulation: Implications for the Fundamentals of Biomolecular Interactions.

The SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing for the virus to invade human cells much faster and with an increased efficiency. In particular, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain, including the effect of double mutation, and compare the results with the wild type. We have recently developed a method of calculating the amino-acid-amino-acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant finding is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.

Mutations of Omicron Variant at the Interface of the Receptor Domain Motif and Human Angiotensin-Converting Enzyme-2.

The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with a large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense, and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and the human angiotensin-converting enzyme-2 (ACE2) interface, we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU) indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge, which facilitates the interaction with ACE2. We have identified changes in bonding due to mutations in the RBM. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.

Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors.

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

First-Principles Simulation of Dielectric Function in Biomolecules.

The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2-5.7 eV and 14.4-15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.

Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation.

The spike protein of SARS-CoV-2 binds to the ACE2 receptor via its receptor-binding domain (RBD), with the RBD-ACE2 complex presenting an essential molecular target for vaccine development to stall the virus infection proliferation. The computational analyses at molecular, amino acid (AA), and atomic levels have been performed systematically to identify the key interacting AAs in the formation of the RBD-ACE2 complex for SARS-CoV and SARS-CoV-2 with its Alpha and Beta variants. Our study uses the molecular dynamics (MD) simulations with the molecular mechanics generalized Born surface area (MM-GBSA) method to predict the binding free energy (BFE) and to determine the actual interacting AAs, as well as two ab initio quantum chemical protocols based on the density functional theory (DFT) implementation. Based on MD results, Q493, Y505, Q498, N501, T500, N487, Y449, F486, K417, Y489, F456, Y495, and L455 have been identified as hotspots in SARS-CoV-2 RBD, while those in ACE2 are K353, K31, D30, D355, H34, D38, Q24, T27, Y83, Y41, and E35. RBD with Alpha and Beta variants has slightly different interacting AAs due to N501Y mutation. Both the electrostatic and hydrophobic interactions are the main driving force to form the AA-AA binding pairs. We confirm that Q493, Q498, N501, F486, K417, and F456 in RBD are the key residues responsible for the tight binding of SARS-CoV-2 with ACE2 compared to SARS-CoV. RBD with the Alpha variant binds with ACE2 stronger than the wild-type RBD or Beta. In the Beta variant, K417N reduces the binding, E484K slightly enhances it, and N501Y significantly increases it as in Alpha. The DFT results reveal that N487, Q493, Y449, T500, G496, G446, and G502 in RBD of SARS2 form pairs via specific hydrogen bonding with Q24, H34, E35, D38, Y41, Q42, and K353 in ACE2.

Amino acid interacting network in the receptor-binding domain of SARS-CoV-2 spike protein.

The relation between amino acid (AA) sequence and biologically active conformation controls the process of polypeptide chains folding into three-dimensional (3d) protein structures. The recent achievements in the resolution achieved in cryo-electron microscopy coupled with improvements in computational methodologies have accelerated the analysis of structures and properties of proteins. However, the detailed interaction between AAs has not been fully elucidated. Herein, we present a de novo method to evaluate inter-amino acid interactions based on the concept of accurately evaluating the amino acid bond pairs (AABP). The results obtained enabled the identification of complex 3d long-range interconnected AA interacting network in proteins. The method is applied to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. We show that although nearest-neighbor AAs in the primary sequence have large AABP, other nonlocal AAs make substantial contribution to AABP with significant participation of both covalent and hydrogen bonding. Detailed analysis of AABP in RBD reveals the pivotal role they play in sequence conservation with profound implications on residue mutations and for therapeutic drug design. This approach could be easily applied to many other proteins of biomedical interest in life sciences.

Ultra-large-scale ab initio quantum chemical computation of bio-molecular systems: The case of spike protein of SARS-CoV-2 virus.

The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-molecular bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

Intra- and intermolecular atomic-scale interactions in the receptor binding domain of SARS-CoV-2 spike protein: implication for ACE2 receptor binding.

The COVID-19 pandemic poses a severe threat to human health with unprecedented social and economic disruption. Spike (S) glycoprotein in the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the early contact with the ACE2 receptor in the human cell. The subunit S1 in chain A of S-protein has four structural domains: the receptor binding domain (RBD), the n-terminal domain (NTD) and two subdomains (SD1, SD2). We report details of the intra- and inter-molecular binding mechanism of RBD using density functional theory, including electronic structure, interatomic bonding and partial charge distribution. We identify five strong hydrogen bonds and analyze their roles in binding. This provides a pathway to a quantum-chemical understanding of the interaction between the S-protein and the ACE2 receptor with insights into the function of conserved features in the ACE2 receptor binding domain that could inform vaccine and drug development.