Frontiers in Computational Chemistry: Volume 4

By Bentham Science Publishers

Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity. The fourth volume of this series features four chapters covering natural lead compounds, computer aided drug discovery methods in Parkinson’s Disease therapy, studies of aminoacyl tRNA synthetase inhibition in bacteria, computational modeling of halogen bonds in biological systems and molecular classification of caffeine and its metabolites.

• Language: English
• Publisher: Bentham Science Publishers
• Release date: Oct 3, 2018
• ISBN: 9781681084411

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Natural Lead Compounds and Strategies for Optimization

Dev Bukhsh Singh*

Department of Biotechnology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India

Abstract

Natural lead is a chemical compound derived from living organism. Nature provides a vast set of structurally diverse compounds that can be used as a medicine. Traditional knowledge of natural medicine will remain as an important source of future medicine and therapeutics. A lead compound in drug discovery possesses some therapeutic applicability, but it may require a series of structural changes to serve as a drug. The chemical structure of the lead molecule is used as a starting point for chemical modifications in order to improve its selectivity, potency, pharmacodynamics and pharmacokinetic parameters. The high-throughput screening (HTS) techniques are used to screen thousands of compounds to identify potential drug candidates for a given drug target. The structure-activity relationship (SAR) and absorption, distribution, metabolisms, excretion and toxicity (ADMET) parameters and other related drug-likeness properties of a lead can be optimized to discover a potential drug. ADMET assays measure and define the properties such as the rate of metabolism, non-specific and plasma-protein binding, permeability, liver and kidney toxicity, LogP and solubility. Furthermore, the process of lead optimization improves the poor drug-likeness of the lead and a new candidate drug can be recommended for in vitro or clinical testing.

Keywords: ADMET, Drug, Drug Designing, Lead Compound, Medicinal, Natural, Optimization.

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* Corresponding author Dev Bukhsh Singh: Department of Biotechnology, Institute of Biosciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kanpur, India-208024; Tel: [phone]; E-mail: [e-mail]

INTRODUCTION

According to the World Health Organization (WHO), health is a state of complete physical, mental and social well-being, not merely the absence of disease or infirmity [1]. A disease may be defined as a particular abnormal condition which adversely affects a part or all of the organism. Drugs have the capability to restore imbalance or disequilibrium leading to the cure of disease. There are different categories of diseases based on metabolism, immune system, inheritance,

pregnancy, injury, infection and environmentally acquired disorders. A drug is a chemical substance required for the treatment, cure, diagnosis or prevention of disease or to promote good health status. There are different types of drugs-depending on their nature and response. Nature is one of the major sources of medicinal agents for thousands of years [2]. This chapter describes the role of natural compounds in drug discovery process, with a focus on lead discovery and lead optimization strategies. Plant-based traditional medicine system (80% population) plays a very important and essential role in health care. A number of phytochemicals are present in the plants which act as cell modifiers in the human system. One or more parts of the medicinal plants contain different compounds that can be used for the therapeutic purpose [3]. A majority of drugs have been developed from natural plant metabolite or derived from the compounds from natural sources. There are many plant-derived substances such as curcumin, piperin and many others, for which a number of drug targets are available in the human body.

United Nations Convention on Biological Diversity confirms the rights of source nations over their genetic materials and also promotes the protection of local and indigenous knowledge, practices, and innovations. The medicinal roles of phytochemicals from many plants have been reported, and are in use as a medicine against many diseases [4]. These phytochemicals are phenolics, polyphenols, quinones, flavones, flavonols, flavonoids, coumarins, terpenoids and oils, alkaloids, lectins and polypeptides, glycosides and others. Phytochemicals stimulate the physiological activities of the human system and generate a wide range of pharmacological response. Phytochemicals form a complex with target proteins through forces such as hydrogen bonding, hydrophobic interaction and covalent bonding, and produce a pharmacological response [5]. Inhibition or activation of a drug target or modulation of a disease related pathway results in a therapeutic effect in a diseased state. There are many plants which have great potential for the treatment of many diseases but they have not been explored and well documented yet. Natural products and their derivatives are the main sources of structural diversity for the drug discovery process [6]. A natural product is a chemical compound produced by living organism in nature that has some biological activity. It can be extracted from the tissues of plants, animals, marine organism or microbes. Natural products can be extracted as such or can be synthesized. Synthesis of many natural products is difficult and is expensive to produce them at a large scale. Most of the clinically used therapeutics is being produced by in vitro chemical synthesis. It is difficult to synthesise structurally complex metabolites such as taxol and vincristine by in vitro synthesis [7].

Therapeutic efficacy of the leads can be optimized to achieve a high pharmacological response on treatment. Lead compounds should have good potency and specificity for a drug target so that they can be transformed into an active drug after lead optimization. Lead optimization improves the specificity and selectivity of a chemical compound for drug target, pharmacodynamics and to develop a potential drug candidate.

KEY STAGES IN DRUG DISCOVERY PROCESS

Drug discovery programme is necessary to find the therapeutic solution for a disease. Drug discovery process includes identification and validation of drug target, assay development, lead identification and optimization, screening and identification of potential drug candidate, clinical trial, and feedback, and approval of drug and marketing (Fig. 1). A drug fails if it does not generate therapeutics response or has a toxic effect on human. Target identification and validation is the most important step in the development of a drug. It enables us to predict the response of a drug and explore the mechanism-based side effects. A broad class of biological entities such as proteins, nucleic acids, carbohydrates, and lipids can serve as drug targets. Gene or gene products also interact with drugs. Drugs should be designed keeping in mind the proteins, enzymes or receptors related to ADMET properties to achieve the maximum therapeutic benefits. Druggable genome defines the set of genes that encode promising drug targets. Identification of druggable genes in various diseases can help the process of drug development. Genome-wide association studies (GWAS) help in identification of druggable targets and its interaction with the drugs.

Fig. (1))

Key steps in modern drug development process.

A potential drug target needs to be safe, efficacious, specific and druggable. Biomedical data mining using bioinformatics approaches helps in identification, selection, and validation of potential disease targets. Differential expression of an mRNA or protein in normal and diseased condition also enables us to identify a drug target. A drug target can be validated through multiple approaches to increase the confidence level [8]. Antisense technology is a powerful approach which involves binding of an antisense molecule to target mRNA and prevents the related protein synthesis. In contrast to gene knock out approach, the effect of an antisense approach is reversible. Monoclonal antibodies are also used for target validation as they interact with the large region of the target protein. Chemical genomics is the study of genomic response to a chemical compound [9]. This approach is also very useful in identification and validation of a drug target.

Compound screening assays for a disease are developed during hit identification and lead discovery process of drug designing. Hit is a compound which shows the desired activity in screen but it needs to be tested further. Exploitation of drug-like compound databases and database of target genes and proteins facilitates the designing of new chemical entities through molecular modeling approach [10]. High throughput screening has the capability to screen the entire library of compounds against a target in a complex assay system. Knowledge-based screening selects a small subset of compounds from a library that may have activity against a target protein based on scientific and literature knowledge. Cell-based assays have been applied to membrane receptors, ion channels, and nuclear receptors to assess the activity of compounds [11]. Biochemical assays are applied to both receptors and enzyme targets which measure the affinity of a compound with the target protein. A plethora of assays is available and the choice of assay formats mainly depends upon the nature of drug target. During an assay selection, the pharmacological relevance of assay, reproducibility, quality, cost and effect of a compound in the assay should be considered as important points [12].

Once a number of hits have been obtained, then it becomes very important and decisive to define which compound is best to work on. Drug discovery tools are used to cluster entire hits based on structural similarity and representative molecules are selected from a diverse set of compounds for further optimization. Drug discovery process should be initiated with a small molecule as lead optimization may increase molecular weight. Traditional medicine system promotes the plant-based drug discovery process through investigation of leads from natural sources [13]. The main objective of lead optimization is to develop more potent and selective compounds which possess desired pharmacokinetic activity in vivo model. Structure-based drug designing techniques can be applied to find the information of binding site on target protein.

Molecular docking techniques are employed to find the top scoring compounds that have a high binding affinity for the binding site of target protein [14]. Computational chemistry tools speed up the process of drug discovery by playing a very significant role in modeling, designing, searching of analogues, pharma- cophore mapping, pharmacophore based searching, virtual screening, molecular dynamics simulation, pharmacokinetics and pharmacodynamics studies. Eval- uation of absorption, distribution, metabolism, and toxicity (ADMET) parameters are very important for a compound to qualify as a drug. Once candidate drugs are determined, they are subjected to different stages of the clinical trial to ensure its efficacy and non-toxic response in the human. A drug needs to be approved by drug administration authority before its large-scale synthesis and release into the market. Advances in the synthetic chemistry enable the chemical synthesis of many elucidated structures [15]. Major side effects of a drug are monitored and reviewed from time to time and its license can be revoked if major adverse effects are reported in the human population. Drugs derived from natural sources have a low chance of failure due to side effects. There are a series of hurdles for a compound must pass to qualify as a drug.

Ligand-based drug designing is based on the interaction between the ligand and target binding site. The structural details of ligand-protein interaction are determined from the crystalline enzyme-inhibitor complex. Binding site and the binding interactions between protein-ligand is determined through computational tools [16]. The cavity in the binding site of receptor-ligand interaction can be located, and a substituent of appropriate size can be created on ligand to fill in the cavity to achieve the extra binding stability. A number of computational tools are available for prediction of cavities or pockets on protein surface where ligand can bind. There may be a number of cavities in a protein but in most of the cases cavity with largest area and volume is associated with the binding site. The accuracy of binding site prediction should be high enough to proceed for molecular docking and virtual screening. Grid-based, sphere-based, α-shape-based and probe energy-based methods are available for cavity or pocket prediction. A large number of analogues or similar compounds are designed and docking approaches are used to find the fitness and binding capacity of these compounds into binding site. In de novo designing, the structural detail of binding between ligand and enzyme is determined by x-ray crystallography [17]. Potential binding regions in the binding site of the enzyme is identified by removing the ligand. A lead compound is searched, designed and synthesized to test the selectivity and activity for the target enzyme. The complex of a lead compound with the target enzyme is crystallized to find the actual binding information. After this step, a structure-based drug designing is applied.

ROUTE OF A DRUG AND ITS FATE

Absorption of drug depends on the ionization of drug and surface area of stomach and intestine. The surface area of the intestine is much larger and permeable than stomach, thus it provides fast and efficient drug absorption. The stomach (low pH) favors the high undissociated concentration of acidic drug compared to high pH of the intestine [18]. Weakly acidic drugs are more readily absorbed by an acidic environment than weakly basic drugs. Oral absorption of drug depends on physicochemical and biopharmaceutical properties of the drug [19]. It is expected that orally active drug should satisfy the Lipinski rule of five to achieve high biological activity. This rule describes the pharmacokinetics (ADME) of a drug, therefore, Lipinski parameters should keep in mind during lead optimization. Route of a drug and its fate in the human body has been represented in the Fig. (2). Drug solubility, dissolution, and permeability across the route are the key factors controlling the drug absorption. Intestinal absorption of drugs in human can be predicted by theoretical computation of 2D molecular descriptors related to physicochemical properties such as lipophilicity, polarity, polarizability, and hydrogen bonding [20]. Hydrogen bonding properties have the largest impact on drug absorption and should be kept to a minimum to achieve high absorption. Low uptake of the drug in human increases the risk of side effects and toxicity. Oral bioavailability is one of the properties that need to be optimized. Absorption of a compound can be enhanced by changing the physicochemical properties of lead through lead optimization.

Fig. (2))

Route of a drug and its fate in the human body after oral administration.

After absorption, a drug enters in the systemic circulation for its distribution to tissues of the body. Drug distribution is the process of delivering a drug molecule from the blood circulatory system to tissues of body and especially to the site of action [21]. Distribution of a drug depends on its lipophilicity, molecular size, degree of ionization, protein binding and affinity to other molecules. The greater the lipophilicity, the more is the distribution and vice versa. Smaller size drugs are more rapidly distributed than larger size drugs. The degree of ionization also affects the drug distribution because drugs can be trapped in a specific compartment when exists in ionized forms [22]. Different blood-brain barriers are present in the route of distribution which significantly decreases the degree of distribution. Endothelial cells, pericytes, and glial cells form the barriers in the passage of drug. Plasma proteins such as albumin, globulins, glycoproteins and lipoproteins bind with specific drugs [23]. Albumin is the most abundant plasma protein and it binds to acidic drugs. Drug distribution is described by the apparent volume of distribution which measures the relative distribution of a drug between tissue and plasma [24]. A drug should be selective to the target; otherwise, it will recognize off-targets in the body which may lead to toxicity.

Drug metabolism is the process of breakdown of drugs into active substances. Liver is the primary site of drug metabolism. Liver plays a major role in metabolism, digestion, detoxification, and elimination of chemical substances. The family of liver isoenzymes known as cytochrome P-450 (CYP) converts the drug into other metabolites. These metabolites bind with other substances for excretion through the lungs, saliva, sweat, urine or breast milk or may be reabsorbed in the intestine [25]. There are about 30 CYP enzymes, out of which CYP1A2, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4 are the major metabolizing enzymes [26]. CYP3A4 are the most important and clinically important enzymes in human. They metabolize nearly 50% of the drugs [27]. Knowledge of metabolic pathway, metabolite stability, toxicity and enzymes involved in drug metabolism is an important information in the process of drug development.

The rate of metabolism affects the oral bioavailability and elimination of drug in human. Structural modification of drug candidate can alter the drug metabolism. Highly lipophilic or highly hydrophilic drugs are not suitable because of poor bioavailability and poor excretion. Prior information on drug metabolism can guide the researcher to introduce a functional group which will alter metabolic stability as per requirement [28]. Replacing an active group with a non-reactive group can increase the metabolic stability. For example, replacing a methyl group with a t-butyl group can prevent demethylation.

LEAD DISCOVERY

In lead discovery, active new chemical entities are determined, which by lead optimization may be transformed into a clinically useful drug. Lead compounds should have desired potency and selectivity for the target. Synthesis of a lead compound should be easy and is should be amenable to chemical modification. Its formulation should not be problematic. The drug should be easily converted into the pill, gel, cream suitable for treatment condition. It should be free from structural elements that provoke toxicity; for example, alkylating agents and Michael acceptors [29]. A lead compound can be identified through the following routes: 1) By chance observations of a compound in study (Example: Penicillin) 2) optimizing the side effects of a compounds 3) Knowledge from herbal / folk remedies 4) Screening of product metabolites from natural sources 5) High throughput screening of compound libraries 6) Rational drug design 7) Natural substrate-based drug design. It requires a lot of effort to transform a lead compound into a drug candidate.

A lead compound with inappropriate distribution parameters can be improved by the process of lead optimization. Physicochemical and biochemical properties such as solubility, permeability, and metabolic stability determine the pharmacokinetics of a drug [30]. Physicochemical and biochemical properties of a compound are very useful in guiding the structural changes required to improve drug-likeness. Attention should be paid on optimizing those properties which allow the discovery of a candidate that possess all the qualities of a successful drug. Approximately 39% drugs fail in the development process because of poor bioavailability and pharmacokinetic properties.

Natural Lead

There are many known drugs that cause a little or more side effects in human. The folk or herbal remedies serve as useful starting points for the identification of lead compounds. It is exciting that 80% of the world’s population uses the drugs derived from natural sources [31]. Another interesting fact is that about 35% of drugs have key structural elements of natural origin. There is a broad scope of natural lead compounds because only 5% of the 500,000 higher plant species have been studied for their pharmacology [32]. Each plant contains potentially 10,000 different constituents.

The active components and pharmacological response of the rest of the herbal plants can be explored to achieve the goal of drug discovery. Each plant has potentially many thousand different constituents. Many drugs are derived from natural products and that natural compounds have served as excellent lead compounds. Natural compound screening is a widely used method to find lead compounds. Plant and animal extracts, marine organisms, microbial products are used in biological assays to find some biological activity [33]. For this purpose, a target is identified and a bioassay is developed. In case of a positive hit, the active constituent is isolated from the herbal extract to serve as a lead compound. One of the advantages of natural product screening is that nature provides a vast set of structurally diverse compounds. In drug discovery process, more priority is given to the lead compounds derived from natural sources. List of some natural leads their sources and therapeutic applications have been listed in the Table 1 [7, 34]. 2D structure of some natural lead compounds are shown in Fig. (3).

Fig. (3))

2D structure of some natural lead compounds.

Table 1 List of some natural lead compounds their sources and therapeutic applications

There are some problems associated with natural products screening. The herbal extracts are often very complex and contain many diverse and large macromolecules such as carbohydrates, lipids, and proteins [35]. It is very problematic to isolate an active component of herbal mixture present in a very small amount. Isolation and structure determination of a compound is also a difficult and laborious task. Sometimes synthesis of the compound becomes challenging [36]. Identification of pharmacophore is also a complex task. A pharmacophore is the key structural element of a compound required for its biological activity.

Therapeutic Role of Some Natural Leads

Curcumin

Curcumin is a secondary metabolite of turmeric, derived from Curcuma longa L. Curcumin has a plethora of targets and has many biological activities. Several curcumin derivatives have been synthesized and their mechanisms of action related to different pharmacological responses have been discovered [37]. Curcumin has been reported to possess antitumor, antiviral, antibacterial, antifungal, anti-inflammatory, antioxidant, neuroprotective, anti-aging and other therapeutic properties [38, 39]. Curcumin inhibits the arachidonic acid metabolism, lipoxygenase, cyclooxygenase, cytokines, Nuclear factor-kB and release of steroidal hormones. Curcumin stabilizes the lysosomal membrane and causes uncoupling of oxidative phosphorylation which is responsible for its anti-inflammatory response [40]. Curcumin has shown binding to numerous inflammatory molecules (tumor necrosis factor α, cyclooxygenase, α1-acid glycoprotein and myeloid differentiation protein 2), cell survival proteins, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca²+ ATPase, DNA methyltransferases 1, DNA polymerase λ, Ribonuclease A, lipoxygenase, matrix metalloproteinases, lysozyme, protein kinases (protein kinase C, viral sarcoma, gylycogen synthase, kinase-3β, ErbB2 and phosphorylase kinase), protein reductases (thioredoxin reductase and aldose reductase), carrier proteins (casein, albumin, fibrinogen, β-lactoglobulin and immunoglobulin), FtsZ protofilaments, transthyretin, tubulin, aminopeptidase N, β-amyloid aggregates, glutathione, prion protein, DNA, RNA and metal ions [41].

Piperin

Black pepper (Piper nigrum) is most commonly used spice in human diets for several thousands of years [42]. It is also used as a medicine, preservative, and perfume. Piperine is an active phenolic component of black pepper. It stimulates the digestive enzymes of the pancreas, lowers lipid peroxidation, acts as an antioxidant, and enhances the bioavailability of therapeutic drugs [43]. Another natural compound gaultherin, a salicylate derivative extracted from Gaultheria yunnanensis, has also been reported to have analgesic and anti-inflammatory effects and lack gastric ulcerogenic effect compared to aspirin [44]. The anti-inflammatory activities of piperin have been demonstrated in rat models. Studies have shown the in vitro inhibitory activity of piperin against the enzymes responsible for leukotriene and prostaglandin biosynthesis, 5-lipoxygenase and COX-1, respectively [45]. Piperin can be beneficial for the treatment of inflammatory diseases such as rheumatoid arthritis. Rheumatoid arthritis is characterized by inflammatory immune cell infiltration into