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Deep learning-based design and experimental validation of a medicine-like human antibody library.
Brief Bioinform
November 2024
Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceutical Inc., 900 Ridgebury Road, Ridgefield, CT 06877, United States.
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain along with the advent of generative deep learning algorithms raises the possibility of computationally generating novel antibody sequences with desirable developability attributes. Here, we describe a deep learning model for computationally generating libraries of highly human antibody variable regions whose intrinsic physicochemical properties resemble those of the variable regions of the marketed antibody-based biotherapeutics (medicine-likeness).
View Article and Find Full Text PDFSynthetic cells in tissue engineering.
Curr Opin Biotechnol
January 2025
INM - Leibniz Institute for New Materials, Campus D2 2, 66123 Saarbrücken, Germany; Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Campus E8 1, 66123 Saarbrücken, Germany; Center for Biophysics, Saarland University, Campus Saarland, 66123 Saarbrücken, Germany; Max Planck Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, United Kingdom. Electronic address:
Tissue functions rely on complex structural, biochemical, and biomechanical cues that guide cellular behavior and organization. Synthetic cells, a promising new class of biomaterials, hold significant potential for mimicking these tissue properties using simplified, nonliving building blocks. Advanced synthetic cell models have already shown utility in biotechnology and immunology, including applications in cancer targeting and antigen presentation.
View Article and Find Full Text PDFStructural insights into glucose-6-phosphate recognition and hydrolysis by human G6PC1.
Proc Natl Acad Sci U S A
January 2025
Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
The glucose-6-phosphatase (G6Pase) is an integral membrane protein that catalyzes the hydrolysis of glucose-6-phosphate (G6P) in the endoplasmic reticulum lumen and plays a vital role in glucose homeostasis. Dysregulation or genetic mutations of G6Pase are associated with diabetes and glycogen storage disease 1a (GSD-1a). Studies have characterized the biophysical and biochemical properties of G6Pase; however, the structure and substrate recognition mechanism of G6Pase remain unclear.
View Article and Find Full Text PDFAlteration of the Catalytic Properties of the Epoxyalcohol Synthase CYP443D1 (NvEAS) of the Starlet Sea Anemone Nematostella vectensis as a Result of a Single Amino Acid Substitution.
Dokl Biochem Biophys
January 2025
Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences,", 420111, Kazan, Russia.
Cytochromes of the P450 superfamily are widespread in nature; they were found in all studied aerobic organisms. Although the degree of similarity between cytochromes P450 of different families is low, all enzymes of this superfamily have similar tertiary structures. In addition, all cytochromes P450, including enzymes of the CYP74 clan, contain substrate recognition sites in their sequences, which form the catalytic center.
View Article and Find Full Text PDFIdentification of promising dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B inhibitors from selected terpenoids through molecular modeling.
Bioinform Adv
December 2024
Structural and Computational Biology Group, Nutritional and Industrial Biochemistry Research Unit, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria.
Motivation: Investigating novel drug-target interactions is crucial for expanding the chemical space of emerging therapeutic targets in human diseases. Herein, we explored the interactions of dipeptidyl peptidase-4 and protein tyrosine phosphatase 1B with selected terpenoids from African antidiabetic plants.
Results: Using molecular docking, molecular dynamics simulations, molecular mechanics with generalized Born and surface area solvation-free energy, and density functional theory analyses, the study revealed dipeptidyl peptidase-4 as a promising target.
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