Domain-aware machine learning (ML) models have been increasingly adopted for accelerating small molecule therapeutic design in the recent years . These models have been enabled by significant advancement in state-of-the-art artificial intelligence (AI) and computing infrastructures . Several ML architectures are pre-dominantly and independently used either for predicting the properties of small molecules, or for generating lead therapeutic candidates . Synergetically using these individual components along with robust representation and data generation techniques autonomously in closed loops holds enormous promise for accelerated drug design which is a time consuming and expensive task otherwise . In this perspective, we present the most recent breakthrough achieved by each of the components, and how such autonomous AI and ML workflow can be realized to radically accelerate the hit identification and lead optimization . Taken together, this could significantly shorten the timeline for end-to-end antiviral discovery and optimization times to weeks upon the arrival of a novel zoonotic transmission event . Our perspective serves as a guide for researchers to practice autonomous molecular design in therapeutic discovery.