We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids.First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules.Then, we follow the framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the clean molecule by denoising the noisy grid with a single step.Our method,, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm.Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are {\em atom-level-based} methods, which consider atoms as basic components and generate atom positions and types. In this way, however, it is hard to generate realistic fragments with complicated structures. To solve this, we propose \textsc{D3FG}, a {\em functional-group-based} diffusion model for pocket-specific molecule generation and elaboration.

The generation of high-quality candidate molecules remains a central challenge in AI-driven drug design. Current phenotype-based and target-based strategies each suffer limitations, either incurring high experimental costs or overlook system-level cellular responses. To bridge this gap, we propose ExMoIRL, a novel generative framework that synergistically integrates phenotypic and target-specific cues for de novo molecular generation. The phenotype-guided generator is first pretrained on expansive drug-induced transcriptional profiles and subsequently fine-tuned via multi-objective reinforcement learning (RL). Crucially, the reward function fuses docking affinity and drug-likeness scores, augmented with ranking loss, prior-likelihood regularization, and entropy maximization. The multi-objective RL steers the model toward chemotypes that are simultaneously potent, diverse, and aligned with the specified phenotypic effects. Extensive experiments demonstrate ExMoIRL's superior performance over state-of-the-art phenotype-based and target-based models across multiple well-characterized targets. Our generated molecules exhibit favorable drug-like properties, high target affinity, and inhibitory potency (IC50) against cancer cells. This unified framework showcases the synergistic potential of combining phenotype-guided and target-aware strategies, offering a more effective solution for de novo drug discovery.

Achieving precise control over a molecule's biological activity-encompassing targeted activation/inhibition, cooperative multi-target modulation, and off-target toxicity mitigation-remains a critical challenge in de novo drug design. However, existing generative methods primarily focus on producing molecules with a single desired activity, lacking integrated mechanisms for the simultaneous management of multiple intended and unintended molecular interactions. Here, we propose ActivityDiff, a generative approach based on the classifier-guidance technique of diffusion models. It leverages separately trained drug-target classifiers for both positive and negative guidance, enabling the model to enhance desired activities while minimizing harmful off-target effects. Experimental results show that ActivityDiff effectively handles essential drug design tasks, including single-/dual-target generation, fragment-constrained dual-target design, selective generation to enhance target specificity, and reduction of off-target effects. These results demonstrate the effectiveness of classifier-guided diffusion in balancing efficacy and safety in molecular design. Overall, our work introduces a novel paradigm for achieving integrated control over molecular activity, and provides ActivityDiff as a versatile and extensible framework.

The de novo generation of drug-like molecules capable of inducing desirable phenotypic changes is receiving increasing attention. However, previous methods predominantly rely on expression profiles to guide molecule generation, but overlook the perturbative effect of the molecules on cellular contexts. To overcome this limitation, we propose SmilesGEN, a novel generative model based on variational autoencoder (VAE) architecture to generate molecules with potential therapeutic effects. SmilesGEN integrates a pre-trained drug VAE (SmilesNet) with an expression profile VAE (ProfileNet), jointly modeling the interplay between drug perturbations and transcriptional responses in a common latent space. Specifically, ProfileNet is imposed to reconstruct pre-treatment expression profiles when eliminating drug-induced perturbations in the latent space, while SmilesNet is informed by desired expression profiles to generate drug-like molecules. Our empirical experiments demonstrate that SmilesGEN outperforms current state-of-the-art models in generating molecules with higher degree of validity, uniqueness, novelty, as well as higher Tanimoto similarity to known ligands targeting the relevant proteins. Moreover, we evaluate SmilesGEN for scaffold-based molecule optimization and generation of therapeutic agents, and confirmed its superior performance in generating molecules with higher similarity to approved drugs. SmilesGEN establishes a robust framework that leverages gene signatures to generate drug-like molecules that hold promising potential to induce desirable cellular phenotypic changes.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids.First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules.Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the "clean" molecule by denoising the noisy grid with a single step.Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm.Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

Developing bioactive molecules remains a central, time- and cost-heavy challenge in drug discovery, particularly for novel targets lacking structural or functional data. Pharmacophore modeling presents an alternative for capturing the key features required for molecular bioactivity against a biological target. In this work, we present PharmaDiff, a pharmacophore-conditioned diffusion model for 3D molecular generation. PharmaDiff employs a transformer-based architecture to integrate an atom-based representation of the 3D pharmacophore into the generative process, enabling the precise generation of 3D molecular graphs that align with predefined pharmacophore hypotheses. Through comprehensive testing, PharmaDiff demonstrates superior performance in matching 3D pharmacophore constraints compared to ligand-based drug design methods. Additionally, it achieves higher docking scores across a range of proteins in structure-based drug design, without the need for target protein structures. By integrating pharmacophore modeling with 3D generative techniques, PharmaDiff offers a powerful and flexible framework for rational drug design.

Drug development is a critical but notoriously resource- and time-consuming process. In this manuscript, we develop a novel generative artificial intelligence (genAI) method DiffSMol to facilitate drug development. DiffSmol generates 3D binding molecules based on the shapes of known ligands. DiffSMol encapsulates geometric details of ligand shapes within pre-trained, expressive shape embeddings and then generates new binding molecules through a diffusion model. DiffSMol further modifies the generated 3D structures iteratively via shape guidance to better resemble the ligand shapes. It also tailors the generated molecules toward optimal binding affinities under the guidance of protein pockets. Here, we show that DiffSMol outperforms the state-of-the-art methods on benchmark datasets. When generating binding molecules resembling ligand shapes, DiffSMol with shape guidance achieves a success rate 61.4%, substantially outperforming the best baseline (11.2%), meanwhile producing molecules with novel molecular graph structures. DiffSMol with pocket guidance also outperforms the best baseline in binding affinities by 13.2%, and even by 17.7% when combined with shape guidance. Case studies for two critical drug targets demonstrate very favorable physicochemical and pharmacokinetic properties of the generated molecules, thus, the potential of DiffSMol in developing promising drug candidates.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids.First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules.Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the "clean" molecule by denoising the noisy grid with a single step.Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm.Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

In recent years, AI-assisted drug design methods have been proposed to generate molecules given the pockets' structures of target proteins. Most of them are {\em atom-level-based} methods, which consider atoms as basic components and generate atom positions and types. In this way, however, it is hard to generate realistic fragments with complicated structures. To solve this, we propose \textsc{D3FG}, a {\em functional-group-based} diffusion model for pocket-specific molecule generation and elaboration. And the two kinds of components can together form complicated fragments that enhance ligand-protein interactions.