Omics Studies in Drug Design

**3**

**Chapter 1**

*Arli Aditya Parikesit*

**1. Introduction**

Introductory Chapter: The

**1.1 Structural bioinformatics contributions in -omics studies**

Emerging Corner of the Omics

Studies for Rational Drug Design

The Acceleration of COVID-19 research in Proteomics and Transcriptomics studies occurred swiftly due to the massive amount of investment and advances in biomanufacturing [1, 2]. Moreover, the repurposing drug research has elicited remdesivir as the FDA-approved drug for COVID-19, despite mixed result from the WHO solidarity trial [3]. More drug leads are also currently undergoing clinical trial as well. This rapid development in the rational drug design is strongly associated with the field of structural bioinformatics. As for now (Early December 2020), there are more than 600 deposited SARS-CoV-2 Protein structures in the PDB (per December 2020, in the http://www.rcsb.org). They are SARS-CoV-2 Proteins with various conformations, and bindings with various ligands [4]. Hence, those proteins structures and their annotated functions are currently subject of the extensive COVID-19 drug development along with hefty investment from the pharmaceutical companies. However, in the other side of the story, non-protein biomolecular structures are currently still off the radar. There are only handful of initiatives for the COVID-19 transcriptomics-based drugs [5–7]. However, drug-based transcriptomics initiatives in canceromics are more mature. Breast cancer transcriptomics-based leads are currently under development [8–10]. That particular progress could be elicited due to the application of structural bioinformatics method for prediction the 2D and 3D model of the nucleic acids [11]. However, massive clinical applications still in favors for the proteomics-based drugs due to the stability of the bioassay experiments. In the area of natural products computation, the only realistic approach is still the proteomics-based one. For instance, propolis, as a resinous material from bees, was a subject of intensive molecular simulation research for its respective compounds constituency as diabetes drug candidates [12]. Hence, the same material also employed for the possibility as COVID-19 leads compound [13]. Moreover, various secondary metabolite sources were also investigated as drug candidates with the molecular simulation research, such as ayurvedic plants of India, and various sources of Chinese herbal medicine [14–18]. In this regard, bioinformaticians should proceed with mindful and prudent manner on the deployment of the molecular docking method as there are validation issues that should be resolved before working on the samples [19, 20]. That includes the utilization of the docking decoys, reiterations of Tc-PLIF value, cross-docking, redocking of the attached ligand, and the refinement of the RMSD parameter [21–25]. However, the easiest validation method is the ligand redocking, provided the structure is exist in the PDB repository. The decoy deployment is the most computationally extensive of all, albeit of its high
