Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants

ABSTRACTAs a consequence of their independent evolutionary origins in apes and Old World monkeys, human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency viruses of the SIVsmm/maclineage express phylogenetically and antigenically distinct envelope glycoproteins. Thus, HIV-1 Env-specific antibodies do not typically cross-react with the Env proteins of SIVsmm/macisolates. Here we show that PGT145, a broadly neutralizing antibody to a quaternary epitope at the V2 apex of HIV-1 Env, directs the lysis of SIVsmm/mac-infected cells by antibody-dependent cellular cytotoxicity (ADCC) but does not neutralize SIVsmm/macinfectivity. Amino acid substitutions in the V2 loop of SIVmac239 corresponding to the epitope for PGT145 in HIV-1 Env modulate sensitivity to this antibody. Whereas a substitution in a conserved N-linked glycosylation site (N171Q) eliminates sensitivity to ADCC, a lysine-to-serine substitution in this region (K180S) increases ADCC and renders the virus susceptible to neutralization. These differences in function correlate with an increase in the affinity of PGT145 binding to Env on the surface of virus-infected cells and to soluble Env trimers. To our knowledge, this represents the first instance of an HIV-1 Env-specific antibody that cross-reacts with SIVsmm/macEnv and illustrates how differences in antibody binding affinity for Env can differentiate sensitivity to ADCC from neutralization.IMPORTANCEHere we show that PGT145, a potent broadly neutralizing antibody to HIV-1, directs the lysis of SIV-infected cells by antibody-dependent cellular cytotoxicity but does not neutralize SIV infectivity. This represents the first instance of cross-reactivity of an HIV-1 Env-specific antibody with SIVsmm/macEnv and reveals that antibody binding affinity can differentiate sensitivity to ADCC from neutralization.

Download Full-text

Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1518405113 ◽

2016 ◽

Vol 113 (16) ◽

pp. 4446-4451 ◽

Cited By ~ 13

Author(s):

Jordan R. Willis ◽

Jessica A. Finn ◽

Bryan Briney ◽

Gopal Sapparapu ◽

Vidisha Singh ◽

...

Keyword(s):

Amino Acid ◽

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Computational Design ◽

Cell Repertoire ◽

B Cell Repertoire ◽

Amino Acid Length ◽

Massive Scale ◽

Amino Acid Mutations ◽

Hiv 1

Development of broadly neutralizing antibodies (bnAbs) against HIV-1 usually requires prolonged infection and induction of Abs with unusual features, such as long heavy-chain complementarity-determining region 3 (HCDR3) loops. Here we sought to determine whether the repertoires of HIV-1–naïve individuals contain Abs with long HCDR3 loops that could mediate HIV-1 neutralization. We interrogated at massive scale the structural properties of long Ab HCDR3 loops in HIV-1–naïve donors, searching for structured HCDR3s similar to those of the HIV-1 bnAb PG9. We determined the nucleotide sequences encoding 2.3 × 107unique HCDR3 amino acid regions from 70 different HIV-1–naïve donors. Of the 26,917 HCDR3 loops with 30-amino acid length identified, we tested 30 for further study that were predicted to have PG9-like structure when chimerized onto PG9. Three of these 30 PG9 chimeras bound to the HIV-1 gp120 monomer, and two were neutralizing. In addition, we found 14 naturally occurring HCDR3 sequences that acquired the ability to bind to the HIV-1 gp120 monomer when adding 2- to 7-amino acid mutations via computational design. Of those 14 designed Abs, 8 neutralized HIV-1, with IC50values ranging from 0.7 to 98 µg/mL. These data suggest that the repertoire of HIV-1–naïve individuals contains rare B cells that encode HCDR3 loops that bind or neutralize HIV-1 when presented on a PG9 background with relatively few or no additional mutations. Long HCDR3 sequences are present in the HIV-naïve B-cell repertoire, suggesting that this class of bnAbs is a favorable target for rationally designed preventative vaccine efforts.

Download Full-text

Computational Design of Thiourea-based Cyclophane Sensors for Small Anions

Australian Journal of Chemistry ◽

10.1071/ch11389 ◽

2012 ◽

Vol 65 (3) ◽

pp. 303 ◽

Cited By ~ 4

Author(s):

Huifang Xie ◽

Ming Wah Wong

Keyword(s):

Molecular Dynamics ◽

Binding Affinity ◽

Density Functional ◽

Computational Design ◽

Binding Pocket ◽

Solvent Medium ◽

Guest Binding ◽

Molecular Dynamics Calculations ◽

Anion Complexes ◽

Dynamics Simulations

The host–guest binding properties of a tri-thiourea cyclophane receptor (1) with several common anions have been investigated using density functional theory (DFT) and molecular dynamics calculations. Receptor 1 is predicted to be an effective receptor for binding small halogen and Y-shaped (NO3– and AcO–) anions in the gas phase, cyclohexane and chloroform. The calculated order of anion binding affinity for the receptor 1 in chloroform is F– > Cl– > AcO– > NO3– >Br– > H2PO4– > HSO4–. The binding free energies are strongly influenced by a dielectric solvent medium. The structures of the receptor–anion complexes are characterized by multiple (typically 6) hydrogen bonds in all cases. The overall binding affinity of various anions is determined by the basicity of anion, size and shape of the binding site, and solvent medium. Explicit chloroform solvent molecular dynamics simulations of selected receptor–anion complexes reveal that the anions are strongly bound within the binding pocket via hydrogen-bonding interactions to all the receptor protons throughout the simulation. A sulfur analogue of receptor 1 (2), with a larger central cavity, is shown to be a more effective sensor than 1 for small anions. Two different approaches to develop the thiourea-based cyclophane receptor into a chromogenic sensor were examined.

Download Full-text

Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

Molecules ◽

10.3390/molecules26092742 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2742

Author(s):

Sadaf Shehzad ◽

Rajan Pandey ◽

Pawan Malhotra ◽

Dinesh Gupta

Keyword(s):

Binding Affinity ◽

High Throughput ◽

In Silico ◽

Protein Quality ◽

Simulation Analysis ◽

Computational Design ◽

Cellular Protein ◽

Dynamics Simulation ◽

Stable Complex ◽

In Silico Screening

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.

Download Full-text

Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics

10.21203/rs.3.rs-57159/v1 ◽

2020 ◽

Author(s):

Mauricio Ponga de la Torre

Keyword(s):

Binding Energy ◽

Binding Affinity ◽

Adhesive Strength ◽

Computational Design ◽

Md Simulations ◽

Adhesive Force ◽

S Protein ◽

Angiotensin Converting Enzyme 2 ◽

Target Binding ◽

S Proteins

Abstract The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is e RS = 12.6 ± 1 kCal∙mol-1 with a maximum adhesive force of ~102 pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of R≤60 nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.

Download Full-text

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

10.21203/rs.3.rs-92745/v2 ◽

2021 ◽

Author(s):

Samvedna Saini ◽

Manusmriti Agarwal ◽

Amartya Pradhan ◽

Savitha Pareek ◽

Ashish K Singh ◽

...

Keyword(s):

Binding Affinity ◽

In Silico ◽

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Affinity Maturation ◽

Antibody Engineering ◽

Site Directed Mutagenesis ◽

Dynamics Simulation ◽

Directed Mutagenesis ◽

Human Antibody

Abstract Introduction: Computational antibody engineering, affinity maturation, and screening greatly aid in vaccine and therapeutic antibody development by increasing the speed and accuracy of predictions. This study presents a protocol for designing affinity enhancing mutants of antibodies through in silico mutagenesis. A SARS-CoV-2 cross-reactive neutralizing antibody, CR3022, is considered as a case study.Methods: Our study aimed at generating antibody candidates from the human antibody CR3022 (derived from convalescent SARS patient) against the RBD of SARS-CoV-2 via in silico affinity maturation using site-directed mutagenesis in mutation hotspots. We optimized the paratope of the CR3022 antibody towards the RBD of SARS-CoV-2 for better binding affinity and stability, employing molecular modeling, docking, dynamics simulations, and molecular mechanics energies combined with generalized Born and surface area (MM-GBSA). Results: Nine antibody candidates were generated post in silico site-directed mutagenesis followed by preliminary screening. Molecular dynamics simulation of 100 nanoseconds and MM-GBSA analysis confirmed L-K45S as a lead antibody with the highest binding affinity against the RBD compared to wild-type and mutant counterparts. Three out of the remaining mutants were also found to have distinct epitopes and binding, possessing a potential to be developed against emerging SARS-CoV-2 variants of concern. Conclusion: The study demonstrates the use of an integrative antibody engineering protocol for enhancing affinity and neutralization potential through mutagenesis using robust open-source computational tools and predictors. This study highlights unique scoring and ranking methods for evaluating docking efficiency. It also underscores the importance of framework mutations for developing broadly neutralizing antibodies.

Download Full-text

Computational redesign of Fab CC12.3 with substantially better predicted binding affinity to SARS-CoV-2 than human ACE2 receptor

Scientific Reports ◽

10.1038/s41598-021-00684-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Wantanee Treewattanawong ◽

Thassanai Sitthiyotha ◽

Surasak Chunsrivirot

Keyword(s):

Binding Affinity ◽

Protein Design ◽

Neutralizing Antibodies ◽

Neutralizing Antibody ◽

Binding Affinities ◽

Receptor Binding Domain ◽

Fab Fragment ◽

Angiotensin Converting Enzyme 2 ◽

Large Numbers ◽

Better Than

AbstractSARS-CoV-2 is responsible for COVID-19 pandemic, causing large numbers of cases and deaths. It initiates entry into human cells by binding to the peptidase domain of angiotensin-converting enzyme 2 (ACE2) receptor via its receptor binding domain of S1 subunit of spike protein (SARS-CoV-2-RBD). Employing neutralizing antibodies to prevent binding between SARS-CoV-2-RBD and ACE2 is an effective COVID-19 therapeutic solution. Previous studies found that CC12.3 is a highly potent neutralizing antibody that was isolated from a SARS-CoV-2 infected patient, and its Fab fragment (Fab CC12.3) bound to SARS-CoV-2-RBD with comparable binding affinity to ACE2. To enhance its binding affinity, we employed computational protein design to redesign all CDRs of Fab CC12.3 and molecular dynamics (MD) to validate their predicted binding affinities by the MM-GBSA method. MD results show that the predicted binding affinities of the three best designed Fabs CC12.3 (CC12.3-D02, CC12.3-D05, and CC12.3-D08) are better than those of Fab CC12.3 and ACE2. Additionally, our results suggest that enhanced binding affinities of CC12.3-D02, CC12.3-D05, and CC12.3-D08 are caused by increased SARS-CoV-2-RBD binding interactions of CDRs L1 and L3. This study redesigned neutralizing antibodies with better predicted binding affinities to SARS-CoV-2-RBD than Fab CC12.3 and ACE2. They are promising candidates as neutralizing antibodies against SARS-CoV-2.

Download Full-text

Tuning the course of evolution on the biophysical fitness landscape of an RNA virus

10.1101/090258 ◽

2016 ◽

Cited By ~ 1

Author(s):

Assaf Rotem ◽

Adrian W.R. Serohijos ◽

Connie B. Chang ◽

Joshua T. Wolfe ◽

Audrey E. Fischer ◽

...

Keyword(s):

Binding Affinity ◽

Fitness Landscape ◽

Rna Virus ◽

Viral Evolution ◽

Quantitative Description ◽

Neutralizing Antibody ◽

Viral Population ◽

Evolutionary Pathway ◽

Evolutionary Forces ◽

Selection For

ABSTRACTPredicting viral evolution remains a major challenge with profound implications for public health. Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics device, the “Evolution Chip”, which propagates millions of independent viral sub-populations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs shape viral evolution.

Download Full-text

Computational Design of Stapled Peptide Inhibitor against SARS-CoV-2 Receptor Binding Domain

10.26434/chemrxiv-2021-kl8rf ◽

2021 ◽

Author(s):

Asha Rani Choudhury ◽

Atanu Maity ◽

Sayantani Chakraborty ◽

Rajarshi Chakrabarti

Keyword(s):

Binding Affinity ◽

Receptor Binding ◽

Computational Design ◽

Binding Domain ◽

Receptor Binding Domain ◽

Conformational Restriction ◽

Stapled Peptides ◽

Stapled Peptide ◽

Free Peptide ◽

The One

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. 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. This raises an urgent requirement to understand the infection mechanism and thereby design therapeutic-based treatment for COVID-19. 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. Therefore, the RBD of SARS-CoV-2 can be used as a target to design therapeutics. 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. Using computer simulation, the mechanism and thermodynamics of the binding of six stapled peptides with RBD have been estimated. Among these, the one with two lactam stapling agents has shown binding affinity, sufficient to overcome RBD-ACE2 binding. 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 in higher binding affinity. 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.

Download Full-text