Lei Li

Danqing Wang, Zeyu Wen, Fei Ye et al. · cmu

Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and do not consider crucial structure information. In this paper, we propose a latent sequence-structure model for designing AMPs (LSSAMP). LSSAMP exploits multi-scale vector quantization in the latent space to represent secondary structures (e.g. alpha helix and beta sheet). By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of antimicrobial activity. Our wet laboratory experiments verified that two of the 21 candidates exhibit strong antimicrobial activity. The code is released at https://github.com/dqwang122/LSSAMP.

Yutong Xie, Chence Shi, Hao Zhou et al.

Searching for novel molecules with desired chemical properties is crucial in drug discovery. Existing work focuses on developing neural models to generate either molecular sequences or chemical graphs. However, it remains a big challenge to find novel and diverse compounds satisfying several properties. In this paper, we propose MARS, a method for multi-objective drug molecule discovery. MARS is based on the idea of generating the chemical candidates by iteratively editing fragments of molecular graphs. To search for high-quality candidates, it employs Markov chain Monte Carlo sampling (MCMC) on molecules with an annealing scheme and an adaptive proposal. To further improve sample efficiency, MARS uses a graph neural network (GNN) to represent and select candidate edits, where the GNN is trained on-the-fly with samples from MCMC. Experiments show that MARS achieves state-of-the-art performance in various multi-objective settings where molecular bio-activity, drug-likeness, and synthesizability are considered. Remarkably, in the most challenging setting where all four objectives are simultaneously optimized, our approach outperforms previous methods significantly in comprehensive evaluations. The code is available at https://github.com/yutxie/mars.