Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design.

A drug discovery and development pipeline is a prolonged and complex process that remains challenging for both computational methods and medicinal chemists and has not been able to be resolved using computational methods. Deep learning has been utilized in various fields and achieved tremendous success in designing novel molecules in the pharmaceutical industry. Herein, we use state-of-the-art techniques to propose a deep neural network, AIMLinker, to rapidly design and generate meaningful drug-like proteolysis targeting chimeras (PROTACs) analogs. The model extracts the structural information from the input fragments and generates linkers to incorporate them. We integrate filters in the model to exclude nondruggable structures guided via protein-protein complexes while retaining molecules with potent chemical properties. The novel PROTACs subsequently pass through molecular docking, taking root-mean-square deviation (RMSD), relative Gibbs free energy (ΔΔGbinding), molecular dynamics (MD) simulation, and free energy perturbation (FEP) calculations as the measurement criteria for testing the robustness and feasibility of the model. The generated novel PROTACs molecules possess similar structural information with superior binding affinity to the binding pockets compared to the existing CRBN-dBET6-BRD4 ternary complexes. We demonstrate the effectiveness of the methodology of leveraging AIMLinker to design novel compounds for PROTACs molecules exhibiting better chemical properties compared to the dBET6 crystal pose.

Slide-free imaging of hematoxylin-eosin stained whole-mount tissues using combined third-harmonic generation and three-photon fluorescence microscopy.

Intraoperative margin assessment of surgical tissues during cancer surgery is clinically important, especially in the case of tissue conserving surgery like Mohs micrographic surgery in which minimization of the surgical area is considered crucial. Frozen pathology is the gold standard of assessing excised tissues for signs of remaining cancerous lesions. The current protocol, however, is time-consuming and labor-intensive. Instead of the complex frozen sectioning, staining, and traditional white light microscopy imaging protocol, optically sectioned histopathological imaging of hematoxylin-eosin stained whole-mount skin tissues with a subfemtoliter resolution is demonstrated by using nonlinear microscopy in this study. With our proposed method, the reagents of staining and the contrast of imaging are fully consistent with the current clinical standard of frozen pathology, thus facilitating rapid intraoperative assessment of surgical tissues for future applications. Image: Slide-free nonlinear microscopy imaging of H&E stained whole-mount skin tissue showing the morphology of sweat glands.

Pathological complete response in pancreatic adenocarcinoma with FOLFIRINOX.

The report describes a patient who presented to our centre with abdominal pain and significant weight loss due to adenocarcinoma of the tail of the pancreas. The cancer was deemed as 'resectable disease associated with morbid surgical outcomes' due to the local involvement of the vessels and adjacent organs. Given the patient's excellent performance status, the patient underwent neoadjuvant chemotherapy with folinic acid, fluorouracil, irinotecan and oxaliplatin to downstage the tumour for less morbid surgical resection. The patient underwent 12 cycles of chemotherapy with serial imaging which demonstrated positive response to treatment and surgical resection was performed. Surgical pathology revealed no residual tumour and imaging was negative for any extrapancreatic tumour metastasis. This is an unusual case as pancreatic malignancy is usually lethal with poor survival outcomes.