Verdon, G. | bioRxiv Science

bioRxiv2025

A deep learning approach for rational affinity maturation of anti-VEGF nanobodies

Nanobodies offer several advantages over conventional antibodies due to their lower immunogenicity, enhanced stability, and superior tissue penetration, making them promising candidates for cancer therapy. In this study, we employ deep learning algorithms to design anti-VEGF nanobodies via affinity maturation. Our approach integrates structure-guided mutational modeling and systematic measurement of binding affinity and stability for rational optimization of Complementarity Determining Regions. In addition, we developed a sequence-based melting temperature predictor for nanobodies, ensuring stability of the designed mutants. Our method achieves energy reductions up to -4.92 kcal/mol. Our melting temperature predictor demonstrated a Pearson correlation coefficient of 0.772. These findings emphasize the potential of computational approaches for nanobody affinity maturation and stability prediction, paving the way for more effective therapeutic designs.

bioinformatics↗

bioRxiv2023

Bipalium admarginatum de Beauchamp, 1933 (Platyhelminthes, Tricladida, Geoplanidae) in Malaysia, with molecular characterisation including the mitogenome

We present here the first observation of Bipalium admarginatum de Beauchamp, 1933 since its original description 90 years ago. Three specimens were found on Perhentian Kecil Island, off Terengganu State, Malaysia and photographed in the field, and two were collected. This report thus includes the first colour photographs published for this species, from a locality close to the type-locality, Tioman Island (which is ca. 200 km south of the locality in this study, on the east coast of Peninsula Malaysia). We describe the external morphology and colour pattern of the species, which correspond well to the original description, itself based only on two preserved specimens. We performed an in-depth molecular characterisation of the species, including its complete mitochondrial genome, the 18S sequence and elongation 1 alpha sequence. In addition, EF1a sequences were also retrieved for 5 additional geoplanid species. No tRNA-Thr could be detected in the mitogenome of B. admarginatum, a lack already reported in several species of geoplanids, but we found a 13 bp sequence that contains the anticodon loop and seems to be conserved among geoplanids and might thus possibly represent a non-canonical undetected tRNA. We discuss the difficulties encountered in trying to reconstruct the cluster of nuclear ribosomal genes, a problem already mentioned for other Triclads. Three phylogenies, based respectively on all mitochondrial proteins, 18S, and EF1a, were computed; the position of B. admarginatum within the Bipaliinae was confirmed in each tree, as sister-group to various bipaliine species according to the sequences available for each tree.

zoology↗