Strategies for the Use of Mixture-Based Synthetic Combinatorial Libraries: Scaffold Ranking, Direct Testing In Vivo, and Enhanced Deconvolution by Computational Methods

2008 ◽  
Vol 10 (1) ◽  
pp. 3-19 ◽  
Author(s):  
Richard A. Houghten ◽  
Clemencia Pinilla ◽  
Marc A. Giulianotti ◽  
Jon R. Appel ◽  
Colette T. Dooley ◽  
...  
Keyword(s):  
Computational Methods ◽  
Combinatorial Libraries ◽  
Direct Testing ◽  
Synthetic Combinatorial Libraries

scholarly journals Improvement of Biophysical Properties and Affinity of a Human Anti-L1CAM Therapeutic Antibody through Antibody Engineering Based on Computational Methods

2021 ◽  
Vol 22 (13) ◽  
pp. 6696
Author(s):  
Heesu Chae ◽  
Seulki Cho ◽  
Munsik Jeong ◽  
Kiyoung Kwon ◽  
Dongwook Choi ◽  
...  
Keyword(s):  
Computational Methods ◽  
Human Monoclonal Antibody ◽  
Antibody Engineering ◽  
Antigen Binding ◽  
Post Translational Modification ◽  
Biophysical Properties ◽  
Preclinical Development ◽  
Cell Bank ◽  
Aggregation Propensity

The biophysical properties of therapeutic antibodies influence their manufacturability, efficacy, and safety. To develop an anti-cancer antibody, we previously generated a human monoclonal antibody (Ab417) that specifically binds to L1 cell adhesion molecule with a high affinity, and we validated its anti-tumor activity and mechanism of action in human cholangiocarcinoma xenograft models. In the present study, we aimed to improve the biophysical properties of Ab417. We designed 20 variants of Ab417 with reduced aggregation propensity, less potential post-translational modification (PTM) motifs, and the lowest predicted immunogenicity using computational methods. Next, we constructed these variants to analyze their expression levels and antigen-binding activities. One variant (Ab612)—which contains six substitutions for reduced surface hydrophobicity, removal of PTM, and change to the germline residue—exhibited an increased expression level and antigen-binding activity compared to Ab417. In further studies, compared to Ab417, Ab612 showed improved biophysical properties, including reduced aggregation propensity, increased stability, higher purification yield, lower pI, higher affinity, and greater in vivo anti-tumor efficacy. Additionally, we generated a highly productive and stable research cell bank (RCB) and scaled up the production process to 50 L, yielding 6.6 g/L of Ab612. The RCB will be used for preclinical development of Ab612.

scholarly journals Synthetic gene regulatory networks in the opportunistic human pathogen Streptococcus pneumoniae

2019 ◽  
Author(s):  
Robin A. Sorg ◽  
Clement Gallay ◽  
Jan-Willem Veening
Keyword(s):  
Gene Expression ◽  
Streptococcus Pneumoniae ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Combinatorial Libraries ◽  
Regulatory Elements ◽  
Expression Control ◽  
Gene Expression Control

AbstractStreptococcus pneumoniae can cause disease in various human tissues and organs, including the ear, the brain, the blood and the lung, and thus in highly diverse and dynamic environments. It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro. Here, we apply synthetic biology methods to reverse-engineer gene expression control in S. pneumoniae. A selection platform is described that allows for straightforward identification of transcriptional regulatory elements out of combinatorial libraries. We present TetR- and LacI-regulated promoters that show expression ranges of four orders of magnitude. Based on these promoters, regulatory networks of higher complexity are assembled, such as logic AND and IMPLY gates. Finally, we demonstrate single-copy genome-integrated toggle switches that give rise to bimodal population distributions. The tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.

Library of libraries: A novel approach in synthetic combinatorial libraries

Peptides ◽  
1995 ◽  
pp. 271-272
Author(s):  
Nikolai F. Sepetov ◽  
Viktor Krchňák ◽  
Magda Staňková ◽  
Kit S. Lam ◽  
Shelly Wade ◽  
...  
Keyword(s):  
Combinatorial Libraries ◽  
Novel Approach ◽  
Synthetic Combinatorial Libraries

scholarly journals Enhanced immune activity of cytotoxic T-lymphocyte epitope analogs derived from positional scanning synthetic combinatorial libraries

Blood ◽  
2001 ◽  
Vol 97 (6) ◽  
pp. 1776-1786 ◽  
Author(s):  
Corinna La Rosa ◽  
Radhika Krishnan ◽  
Susan Markel ◽  
Jonathan P. Schneck ◽  
Richard Houghten ◽  
...  
Keyword(s):  
T Cell ◽  
T Lymphocyte ◽  
Cytotoxic T Lymphocyte ◽  
Combinatorial Libraries ◽  
Peptide Sequence ◽  
Ctl Epitopes ◽  
Ctl Epitope ◽  
Positional Scanning ◽  
Synthetic Combinatorial Libraries

The pp65495-503 cytotoxic T-lymphocyte (CTL) epitope from cytomegalovirus (CMV) is universally recognized among CMV+ individuals who express an allele of the human leukocyte antigen A (HLA-A*0201). The relative binding affinity of the epitope to HLA-A*0201 is moderate, and its increased activity might prove beneficial in its use as a CTL epitope vaccine. A new approach to enhance the activity of T-cell epitopes is the use of positional scanning synthetic combinatorial libraries (PS-SCLs). Using a nonamer PS-SCL, the pp65495-503 epitope was modified after screening a CMV-specific T-cell clone (TCC) (3-3F4) from which the native peptide sequence was derived. Two peptides with amino acid substitutions at P1, P3, P7, and P8 are between 103 and 104 more active than the native epitope. Although the native CTL epitope terminates as a free acid, both tetrasubstituted peptides only function as CTL epitopes when the carboxyl terminus is amidated. Selective substitution of the native sequence based on PS-SCL screening results identified 3 amidated monosubstituted and disubstituted peptides that are better recognized than the native epitope by TCCs from a cohort expressing HLA-A*0201. In vitro stimulation of peripheral blood mononuclear cells with each of the peptide epitope analogs stimulated memory CTLs, which recognized CMV-infected targets among a high percentage of CMV+ individuals. Binding studies of peptide analogs with HLA-Ig (immunoglobulin) dimers and 2 different TCCs correlated with in vitro lysis results. These data suggest that increasing the activity of CTL epitopes while maintaining broad recognition is possible, which holds promise for vaccine development in infectious disease and cancer.

Kinetics of Drug Binding and Residence Time

2019 ◽  
Vol 70 (1) ◽  
pp. 143-171 ◽  
Author(s):  
Mattia Bernetti ◽  
Matteo Masetti ◽  
Walter Rocchia ◽  
Andrea Cavalli
Keyword(s):  
Computational Methods ◽  
Residence Time ◽  
Drug Target ◽  
Early Stage ◽  
Kinetic Constant ◽  
Theoretical Background ◽  
Drug Binding ◽  
Binding Kinetics ◽  
Kinetics Of

The kinetics of drug binding and unbinding is assuming an increasingly crucial role in the long, costly process of bringing a new medicine to patients. For example, the time a drug spends in contact with its biological target is known as residence time (the inverse of the kinetic constant of the drug-target unbinding, 1/ koff). Recent reports suggest that residence time could predict drug efficacy in vivo, perhaps even more effectively than conventional thermodynamic parameters (free energy, enthalpy, entropy). There are many experimental and computational methods for predicting drug-target residence time at an early stage of drug discovery programs. Here, we review and discuss the methodological approaches to estimating drug binding kinetics and residence time. We first introduce the theoretical background of drug binding kinetics from a physicochemical standpoint. We then analyze the recent literature in the field, starting from the experimental methodologies and applications thereof and moving to theoretical and computational approaches to the kinetics of drug binding and unbinding. We acknowledge the central role of molecular dynamics and related methods, which comprise a great number of the computational methods and applications reviewed here. However, we also consider kinetic Monte Carlo. We conclude with the outlook that drug (un)binding kinetics may soon become a go/no go step in the discovery and development of new medicines.

Findings on T cell specificity revealed by synthetic combinatorial libraries

2002 ◽  
Vol 267 (1) ◽  
pp. 79-97 ◽  
Author(s):  
Eva Borràs ◽  
Roland Martin ◽  
Valeria Judkowski ◽  
Jacqueline Shukaliak ◽  
Yingdong Zhao ◽  
...  
Keyword(s):  
T Cell ◽  
Combinatorial Libraries ◽  
Cell Specificity ◽  
Synthetic Combinatorial Libraries

Rapid Identification of Immunostimulatory α-Galactosylceramides Using Synthetic Combinatorial Libraries

2007 ◽  
Vol 9 (6) ◽  
pp. 1084-1093 ◽  
Author(s):  
Qian Li ◽  
Rachel M. Ndonye ◽  
Petr A. Illarionov ◽  
Karl O. A. Yu ◽  
Elliot S. Jerud ◽  
...  
Keyword(s):  
Combinatorial Libraries ◽  
Rapid Identification ◽  
Synthetic Combinatorial Libraries
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