*3.1.1 Phenotypic screening*

*Cheminformatics and Its Applications*

*2.3.2 Chemoproteomics*

**3. Drug discovery**

**3.1 Screening**

Drug discovery based on small molecules focuses on the loss of function of proteins due to the already-occupied binding sites ultimately making the proteins unable to target. In this approach, there is a need of high drug exposure in vivo to avoid target inhibition conditions which may lead to potentially harmful side effects of that drug. Proteolysis-targeting chimeras (PROTACS) use the cellular quality control setup to degrade the selective proteins as their targets. This protein degradation system reduces the quantity of drug to be exposed to the living systems which are to be used for halting the protein functions. These proteins may belong to regulatory

Chemoproteomics is employed as a chemical tool for target identification. It can be used to investigate the signal transductions. This particular field of study has flourished as a key technology to characterize the action mechanism of chemical probes and drugs which can act as pharmacological modulators, hence validating the cellular targets of several therapeutic drug candidates. Chemoproteomics can be further characterized as affinity- and activity-based chemical proteomics [15]. In some cases when probe development is a difficult task, multiple kinase inhibitors

Drug discovery is a hectic multistep procedure comprising of highly systematic

approaches to identify, and characterize different compounds leading towards the development of hits and validate them extensively via utilization of chemical toolsets to attain the status of a commercial therapeutic drug status. The important

There are two fundamental approaches which can be used for the purpose of drug discovery, namely, phenotypic screening and target-based screening.

*A diagram representing the summary of key notes regarding drug discovery from natural products.*

proteins, transcription factors, and scaffolding proteins [13, 14].

are used for targeting the kinome effectively [16].

steps of drug discovery are mentioned in **Figure 2**.

**130**

**Figure 2.**

In the early twentieth century, drug development started with the advancements in pharmacology and synthetic and therapeutic chemistry. In the 1950s and 1960s, enzyme kinetics has provided methods for accurate computation of compound's effectiveness and enzyme competence [17].

Between 1999 and 2008, the US Food and Drug Administration (FDA) approved new drug discovery approaches. During this period, 75 small molecules were discovered and analyzed. Out of these, 28 drugs were discovered through phenotypic selection, and 17 drugs were identified by target dependent selection [18].

"Alemtuzumab" was the first antibody that was been obtained by using hybridoma technology in combination with phenotypic identification. It was previously reported against relapse of multiple sclerosis and chronic lymphocytic leukemia (CLL). The CD44 antigen (cell surface glycoprotein) antagonist, RG7356, was isolated with the help of function F.I.R.S.T™ platform. Therefore, functional assays antibodies were used to check effects on cell signaling, proliferation, and programmed cell death [19].

Large combinatorial antibody libraries are the sources of human monoclonal antibodies, successfully used in medical and phenotypic screening. For example, BI-505 was isolated by using F.I.R.S.T™ platform. Improved versions of antibodies were ultimately used in simulation studies of tumor cell death assay and for selective B-lymphoma cell surface binding. Soon after the isolation of BI-505, its molecular target was identified as ICAM-1, which were found to be involved in apoptosis of B-lymphoma cells. BI-505 has a broad antimyeloma activity [20].

By using phenotypic screening technology, patients can increase their effective antibody response like B-cell repertoire. For example, from a healthcare worker, anti-respiratory syncytial virus (RSV) antibody, D25, was isolated. On the virus coat, D25 neutralizes RSV, and perfusion structure of the F protein was expressed which was not identified by target-based screening [21]. The use of phenotypic screening in various experiments is outlined in **Table 1**.


### **Table 1.**

*Phenotypic screening used in some experiments.*

### *3.1.2 Target-based screening*

Target-based screening of natural compounds and synthetic chemicals is being considered as a significant innovation for anticancer drug development [28]. In 2007, Lysine demethylase 5B (KDM5B) and Histone demethylase were recognized, which are liable for the removal of H3K4me2/3 activation marker. Thus, for cancer therapy, KDM5B is regarded as a promising drug target, but the elevated levels of KDM5B were found in many human cancers [29].

The respiratory chain of *Streptococcus agalactiae* consists of two enzymes; type 2-NADH dehydrogenase (NDH-2) and cytochrome *bd* oxygen reductase. *S. agalactiae* is considered as the primary cause of sepsis and meningitis in neonates as well as considerable cause of pneumonia and urinary tract infection [30]. The difference between phenotypic and target-based screening is shown in **Figure 3**.

Some of the target-based screening methods are mentioned as follows.
