scholarly journals In silico Techniques for Prospecting and Characterizing Monoclonal Antibodies

2020 ◽  
Author(s):  
Tania M. Manieri ◽  
Carolina G. Magalhaes ◽  
Daniela Y. Takata ◽  
João V. Batalha-Carvalho ◽  
Ana M. Moro
Keyword(s):  
Monoclonal Antibodies ◽  
Binding Affinity ◽  
In Silico ◽  
Fusion Proteins ◽  
Antibody Engineering ◽  
Bispecific Antibodies ◽  
Antibody Complex ◽  
Antigen Antibody ◽  
Key Residues ◽  
In Silico Methods

In the past few years, improvement in computational approaches provided faster and less expensive outcomes on the identification, development, and optimization of monoclonal antibodies (mAbs). In silico methods, such as homology modeling, to predict antibody structures, identification of epitope-paratope interactions, and molecular docking are useful to generate 3D structures of the antibody–antigen complexes. It helps identify the key residues involved in the antigen–antibody complex and enable modifications to enhance the antibody binding affinity. Recent advances in computational tools for redesigning antibodies are significant resources to improve antibody biophysical properties, such as binding affinity, solubility, stability, decreasing the timeframe and costs during antibody engineering. The immunobiological market grows continuously with new molecules, both natural and new molecular formats, such as bispecific antibodies, Fc-antibody fusion proteins, and mAb fragments, requiring novel methods for designing, screening, and analyzing. Algorithms and software set the in silico techniques on the innovation frontier.

scholarly journals Potentiating Antigen-Specific Antibody Production with Peptides Obtained from In Silico Screening for High-Affinity against MHC-II

Molecules ◽  
2019 ◽  
Vol 24 (16) ◽  
pp. 2949
Author(s):  
Yoshiro Hanyu ◽  
Yuto Komeiji ◽  
Mieko Kato
Keyword(s):  
Monoclonal Antibodies ◽  
Binding Affinity ◽  
Antibody Production ◽  
Specific Antibody ◽  
In Silico ◽  
Igg Antibody ◽  
Mhc Ii ◽  
High Affinity ◽  
Specific Antibody Production

Monoclonal antibodies with high affinity and specificity are essential for research and clinical purposes, yet remain difficult to produce. Agretope peptides that can potentiate antigen-specific antibody production have been reported recently. Here, we screened in silico for peptides with higher affinity against the agretope binding pocket in the MHC-II. The screening was based on the 3D crystal structure of a complex between MHC-II and a 14-mer peptide consisting of ovalbumin residues 323–339. Using this 14-mer peptide as template, we constructed a library of candidate peptides and screened for those that bound tightly to MHC-II. Peptide sequences that exhibited a higher binding affinity than the original ovalbumin peptide were identified. The peptide with the highest binding affinity was synthesized and its ability to boost antigen-specific antibody production in vivo and in vitro was assessed. In both cases, antigen-specific IgG antibody production was potentiated. Monoclonal antibodies were established by in vitro immunization using this peptide as immunostimulant, confirming the usefulness of such screened peptides for monoclonal antibody production.

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

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.

scholarly journals Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers

2021 ◽  
Author(s):  
Saleh Riahi ◽  
Jae Hyeon Lee ◽  
Shuai Wei ◽  
Robert Cost ◽  
Alessandro Masiero ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
In Silico ◽  
Half Life ◽  
Neutralizing Antibodies ◽  
Binding Domain ◽  
Antibody Engineering ◽  
Receptor Binding Domain ◽  
Effector Functions

Abstract As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here we leverage our expertise in computational antibody engineering to rationally design/engineer three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R, and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS-CoV (but not SARS-CoV-2 except for CR3022). Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV-2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV-2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody induced virus activation or enhancement, we suggest application of NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.

High-Throughput Melanin-Binding Affinity and In Silico Methods to Aid in the Prediction of Drug Exposure in Ocular Tissue

2015 ◽  
Vol 104 (12) ◽  
pp. 3997-4001 ◽  
Author(s):  
John Reilly ◽  
Sarah L. Williams ◽  
Cornelia J. Forster ◽  
Viral Kansara ◽  
Peter End ◽  
...  
Keyword(s):  
Binding Affinity ◽  
High Throughput ◽  
In Silico ◽  
Drug Exposure ◽  
Ocular Tissue ◽  
Melanin Binding ◽  
In Silico Methods

scholarly journals Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers

2021 ◽  
Author(s):  
Saleh Riahi ◽  
Jae Hyeon Lee ◽  
Shuai Wei ◽  
Robert Cost ◽  
Alessandro Masiero ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
In Silico ◽  
Half Life ◽  
Neutralizing Antibodies ◽  
Binding Domain ◽  
Antibody Engineering ◽  
Receptor Binding Domain ◽  
Effector Functions

As the COVID-19 pandemic continues to spread, hundreds of new initiatives including studies on existing medicines are running to fight the disease. To deliver a potentially immediate and lasting treatment to current and emerging SARS-CoV-2 variants, new collaborations and ways of sharing are required to create as many paths forward as possible. Here we leverage our expertise in computational antibody engineering to rationally design/optimize three previously reported SARS-CoV neutralizing antibodies and share our proposal towards anti-SARS-CoV-2 biologics therapeutics. SARS-CoV neutralizing antibodies, m396, 80R, and CR-3022 were chosen as templates due to their diversified epitopes and confirmed neutralization potency against SARS. Structures of variable fragment (Fv) in complex with receptor binding domain (RBD) from SARS-CoV or SARS-CoV2 were subjected to our established in silico antibody engineering platform to improve their binding affinity to SARS-CoV2 and developability profiles. The selected top mutations were ensembled into a focused library for each antibody for further screening. In addition, we convert the selected binders with different epitopes into the trispecific format, aiming to increase potency and to prevent mutational escape. Lastly, to avoid antibody induced virus activation or enhancement, we applied NNAS and DQ mutations to the Fc region to eliminate effector functions and extend half-life.

scholarly journals Kolaviron (Kolaflavanone), apigenin, fisetin as potential Coronavirus inhibitors: In silico investigation

2020 ◽  
Author(s):  
Johnson Olaleye Oladele ◽  
Oyedotun Moses Oyeleke ◽  
Oluwaseun Titilope Oladele ◽  
Boyede Dele Olowookere ◽  
Babatunde Joseph Oso ◽  
...  
Keyword(s):  
In Silico ◽  
Binding Pocket ◽  
Therapeutic Agents ◽  
Drug Resistant ◽  
Human Intestine ◽  
Low Toxicity ◽  
Key Residues ◽  
Toxicity Effects ◽  
In Silico Methods ◽  
Novel Therapeutic

Abstract The outbreak of COVID-19 caused by SARS-CoV-2 is increasing with an alarming rate of associated frightening mortality without no known approved therapy. The emergence of new infectious diseases and increase in frequency of drug resistant viruses demand effective and novel therapeutic agents. This study investigated the putative inhibitory potentials of apigenin, fisetin, kolaflavanone, and remdesivir towards SARS-COV2 major protease (6LU7) using in silico methods. Pharmacodynamics, pharmacokinetics and toxicological profiles of the compounds were also examined using the pkCSM server. All the compounds showed good affinity to the binding pocket of 6LU7. It was observed that kolaflavanone exhibited the highest binding affinity when compared to apigenin, fisetin, and remdesivir. The amino acids ASN238, TYR237, LEU286, and LEU287 were showed as the key residues for kolaflavanone binding to human SARS-COV2 major protease. The Pharmacodynamics and pharmacokinetics results suggested that all the tested compounds have significant drug likeness properties and they could be absorbed through the human intestine. Additionally, all the tested compounds except remdesivir are not hepatoxic and also displayed non or relatively low toxic effects in human. Summarily, the results of this study indicated that all the tested compounds are potential putative inhibitors of SARS-COV2 major protease with no or low toxicity effects. However, further experimental and clinical studies are needed to further explore their activities and validate their efficacies against COVID-19.

Visualization of Antibody Transport in Rat Visceral Yolk-Sac Placenta

1982 ◽  
Vol 40 ◽  
pp. 246-247
Author(s):  
William P. Jollie
Keyword(s):  
Phosphate Buffer ◽  
Yolk Sac ◽  
Female Rats ◽  
Thin Sections ◽  
Visceral Yolk Sac ◽  
Antibody Complex ◽  
Cytochemical Reaction ◽  
Hind Foot ◽  
Antigen Antibody ◽  
Yolk Sac Placenta

A technique has been developed for visualizing antibody against horseradish peroxidase (HRP) in rat visceral yolk sac, the placental membrane across which passive immunity previously has been shown to be transferred from mother to young just prior to birth. Female rats were immunized by injecting both hind foot pads with 1 mg HRP emulsified in complete Freund's adjuvant. They were given a booster of 0.5mg HRP in 0.1 ml normal saline i.v. after one week, then bred and autopsied at selected stages of pregnancy, viz., 12, 1 7 and 22 days post coitum, receiving a second booster, injected as above, five days before autopsy. Yolk sacs were removed surgically and fixed immediately in 2% paraformaldehye, 1% glutaraldehye in 0.1 M phosphate buffer with 0.01% CaCl2 at pH 7.4, room temperature, for 3 hr, rinsed 3X in 0.1 M phosphate buffer plus 5% sucrose, then exposed to 1 mg HRP in 1 ml 0.1 M phosphate buffer at pH 7.4 for 1 hr. They were refixed in aldehydes, as above, for 1 5 min (to assure binding of antigen-antibody complex). Following buffer washes, the tissues were incubated in 3 mg diaminobenzidine tetrahydrochloride and 0.01% H2O2 in 0.05 M Tris-HCl buffer for 30 min. After brief buffer washes, they were postfixed in 2% OsO4. in phosphate buffer at pH 7.4, 4°C for 2 hr, dehydrated through a graded series of ethanols, and embedded in Durcupan. Thin sections were observed and photographed without contrast-enhancement with heavy metals. Cytochemical reaction product marked the site of HRP (i.e., antigen) which, in turn, was present only where it was bound with anti-HRP antibody.

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