Incorporating target-specific pharmacophoric information into deep generative models for fragment elaboration

TE Hadfield, F Imrie, A Merritt, K Birchall… - Journal of chemical …, 2022 - ACS Publications
Despite recent interest in deep generative models for scaffold elaboration, their applicability
to fragment-to-lead campaigns has so far been limited. This is primarily due to their inability …

DeepFrag: a deep convolutional neural network for fragment-based lead optimization

H Green, DR Koes, JD Durrant - Chemical Science, 2021 - pubs.rsc.org
Machine learning has been increasingly applied to the field of computer-aided drug
discovery in recent years, leading to notable advances in binding-affinity prediction, virtual …

Fragment-based approaches identified tecovirimat-competitive novel drug candidate for targeting the F13 protein of the monkeypox virus

Y Ali, H Imtiaz, MM Tahir, F Gul, UAK Saddozai… - Viruses, 2023 - mdpi.com
Monkeypox is a serious public health issue in tropical and subtropical areas. Antivirals that
target monkeypox proteins might lead to more effective and efficient therapy. The F13 …

Scaffold hopping approaches for dual-target antitumor drug discovery: opportunities and challenges

A Mishra, A Thakur, R Sharma, R Onuku… - Expert Opinion on …, 2024 - Taylor & Francis
Introduction Scaffold hopping has emerged as a practical tactic to enrich the synthetic bank
of small molecule antitumor agents. Specifically, it enables the chemist to refine the lead …

SeamDock: an interactive and collaborative online docking resource to assist small compound molecular docking

S Murail, SJ De Vries, J Rey, G Moroy… - Frontiers in Molecular …, 2021 - frontiersin.org
In silico assessment of protein receptor interactions with small ligands is now part of the
standard pipeline for drug discovery, and numerous tools and protocols have been …

Deep Lead Optimization: Leveraging Generative AI for Structural Modification

O Zhang, H Lin, H Zhang, H Zhao, Y Huang… - arXiv preprint arXiv …, 2024 - arxiv.org
The idea of using deep-learning-based molecular generation to accelerate discovery of drug
candidates has attracted extraordinary attention, and many deep generative models have …

BMaps: a web application for fragment-based drug design and compound binding evaluation

DR Bryan, JL Kulp Jr, MK Mahapatra… - Journal of Chemical …, 2023 - ACS Publications
Fragment-based drug design uses data about where, and how strongly, small chemical
fragments bind to proteins, to assemble new drug molecules. Over the past decade, we have …

Efficient hit-to-lead searching of kinase inhibitor chemical space via computational fragment merging

GV Andrianov, WJ Gabriel Ong… - Journal of chemical …, 2021 - ACS Publications
In early-stage drug discovery, the hit-to-lead optimization (or “hit expansion”) stage entails
starting from a newly identified active compound and improving its potency or other …

Exploration of potential inhibitors for SARS‐CoV‐2 Mpro considering its mutants via structure‐based drug design, molecular docking, MD simulations, MM/PBSA, and …

A Ghasemlou, V Uskoković… - Biotechnology and …, 2023 - Wiley Online Library
The main protease (Mpro) of SARS‐COV‐2 plays a vital role in the viral life cycle and
pathogenicity. Due to its specific attributes, this 3‐chymotrypsin like protease can be a …

FragExplorer: GRID-based fragment growing and replacement

S Cross, G Cruciani - Journal of Chemical Information and …, 2022 - ACS Publications
Understanding which chemical modifications can be made to known ligands is a key aspect
of structure-based drug design and one that was pioneered by the software GRID. We …