Artificial Intelligence in Coronavirus Drug and Vaccine Development - Part 1

 

Coronavirus (COVID-19) has wreaked havoc across the world with more than 263 million infected cases and close to 5.2 million deaths as of 1st December 2021. The virus, coming from the family of Coronaviridae with its predecessors Severe Acute Respiratory Disease (SARS) and Middle Eastern Respiratory Syndrome (MERS), emerging in 2002 and 2013, respectively, has impacted human population across geographies with USA, Brazil and India emerging as the leading hotspots with more than 20 million confirmed cases each (USA has actually topped 48 million). Refer Bloomberg for current update on Mapping theCoronavirus Outbreak Across the World.

UPDATE: The Omicron variant — first identified in South Africa — was designated as a variant of concern by the World Health Organization (WHO) recently. It has become the fifth and latest variant of concern to be categorized as such since the start of the COVID-19 pandemic.

A variant of concern has the potential for increased transmissibility, severity of illness or decreased effectiveness of vaccines, treatments and public health measures, according to WHO.

 

 

In recent years, machine learning has revolutionized many fields of science and engineering. It has largely transformed our daily lives, from speech and face recognition to customized targeted advertisements. The power of automatic abstract feature learning, combined with a massive volume of data, has immensely contributed to the successful application of ML. Two of the most impactful areas affected in the medical world are drug and vaccine discovery, in which ML has offered compound property prediction, activity prediction, reaction prediction, and ligand–protein interaction.

 

While hospitals and laboratories worldwide are resorting to trial and error tactics for COVID-19 drug discovery and vaccine development, Virtual Screening (VS) has emerged as a popular method for discovering potent compounds due to the inefficiency of lab-based high throughput screening (HTS). VS for rational drug discovery is essentially an approach that involves computationally targeting a specific biomolecule (e.g., DNA, protein, RNA, lipid) of a cell to inhibit its growth and/or activation. Additionally, conventional vaccine discovery methods have been costly, and it may take many years to develop an appropriate vaccine against a specified pathogen.

 

Over the past decade, artificial intelligence (AI)-based models have revolutionized drug discovery in general. AI has also led to the creation of many Reverse Vaccinology (RV) virtual frameworks, which are generally classified as rule-based filtering models. Machine learning (ML) enables the creation of models that learn and generalize the patterns within the available data and can make inferences from previously unseen data. With the advent of deep learning (DL), the learning procedure can also include automatic feature extraction from raw data. Moreover, it has recently been found that deep learning's feature extraction can result in superior performance compared to other computer-aided models.

 

Machine learning has also improved the field of vaccine design over the past two decades. VaxiJen was the first implementation of ML in RV approaches and has shown promising results for antigen prediction. In addition, the recent development of Vaxign-ML, a web-based RV program leveraging machine learning approaches for bacterial antigen prediction, is a testament to the success of exercising mathematical ML-based in RV. In essence, these pipelines consist of feature extraction, feature selection, data augmentation, and cross-validation implemented to predict vaccine candidates against various bacterial and viral pathogens known to cause infectious disease.

In part 2 of the article, we will dig deeper into the use of AI/ML and Deep Learning methods used in drug and vaccine development for COVID-19.