Modern Methods of Drug Discovery

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Strategies for Identifying Drug Targets

Upon a positive result, scientists are required to conduct safety tests on the selected compounds to establish the mechanism by which the drug is absorbed, distributed, metabolized and excreted. This process termed pharmacokinetics indicates the mechanisms that occur when the therapeutic agent enters the body. If all of the results and optimizations are positive, then lead compounds may become potential candidate drugs Biological diversity and modern genomics are crucial topics leading bioscience in the 21st century, and biodiversity is considered to be increasingly important in this field Indeed, natural products are full of biodiversity, the research of which requires extensive and in-depth experience, particularly in taxonomy, which takes time to accrue.

Pharmaceutical and biotechnology companies must adapt to the immediate need for new medicines and adopt new techniques in order to overcome clinical conditions that cannot be treated using conventional therapies. Hence, looking into the structure-activity relationships of naturally occurring active ingredients may offer a strategy to overcome such medicinal challenges. By contrast, if industries want to contribute to, and take advantage of, the drug discovery process, then they must establish techniques, such as computational chemistry, to achieve more sustainable use of their natural resources.

Industries must realize that although natural products perform important biological functions with a valuable role in the ecosystem, their economic value may be less until their primary utility is exposed and established. To understand the utility and important benefits, pharmaceutical industries must be prepared to contribute actively and financially to the drug discovery process Natural products are considered to be particularly valuable for the production of various precious lead components ranging from simple chemical structures to highly complex structures. Natural metabolites are always superior in terms of biochemical and pharmacological activities when compared with secondary metabolites The current drug discovery processes arising from natural resources is primarily focused on the isolation, purification, screening and discovery of novel drug candidates.

In order to move forward with any potential lead compounds, large scale extraction or biotechnology production is required in order to move the lead compounds forward and make them clinically feasible.

Drug Discovery and Development Process - Clinical Research -

In the revolutionized and highly competitive field of modern pharmaceutical research, natural products can mimic distinctive metabolites of biological functionality such as hormones and naturally occurring ligands 19 as well as possessing great structural diversity, which is necessary for the drug discovery process. To regenerate the interest of the pharmaceutical industry and, in order to be competitive with other advanced drug discovery techniques, natural product research must constantly increase the efficiency of screening computational or otherwise , isolation, robotic separation and purification.

Additionally, drug stability and formulation studies as well as efficacy, pharmacokinetics and metabolic engineering investigations are required in order to identify compounds of interest and move them forward into clinically applicable therapies. The growing demand for medicinal plants in traditional and herbal medicine is also threatening their existence. To improve biodiversity across the globe, it is critical to cultivate medicinal plants using controlled and scientific methods, to provide the desired medicinal plants at high quality.

In addition, toxic waste from the production process greatly impacts the biological ecosystem; it has particularly harmful effects on the plants and aquatic life in streams To protect the natural resources, toxic waste containing toxic elements and unpleasant, odor-producing chemicals must be separated and treated independently. This protection of the natural flora will aid in the sustainability of ecosystems and hence protect any natural resource that may be used for the discovery of unique medicinal and biological metabolites.

An integrative approach of coupling advanced genetic sequencing with the management of biosynthetic pathways, may deliver a sustainable and realistic route for the future discovery of pharmaceutical drug candidates. The success of natural products in past and present drug discovery is fundamentally associated with their complex structural diversity, as well as advancement in understanding of how structural confirmations or functionality contribute to molecular activity in biomedicine.

Nature continues to provide biological diversity, which is important to target, particularly considering the insufficient results obtained from combinatorial techniques.

Drug discovery and development

It is hoped that the environment will continue to provide undiscovered resources, permitting the unique discovery of novel weapons against developing infections. Feher M and Schmidt JM: Property distributions: Differences between drugs, natural products, and molecules from combinatorial chemistry. J Chem Inf Comput Sci. Chin J Nat Med. Elsevier Inc. Butler MS: The role of natural product chemistry in drug discovery.

J Nat Prod. Drug Discov Today. Antibiotics Basel. View Article : Google Scholar. J Neurochem.

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Humana Press Inc. Biochim Biophys Acta. Oshiro BT: The semisynthetic penicillans. Prim Care Update Ob Gyns. Pharmacol Pharm. Once a drug target is identified, whether it be via a specific technique Table 1 or from review of literature, the first step is to repeat the experiment to confirm that it can be successfully reproduced. Introduce variation to the ligand drug -target-environment. Thus, we have to improve on our ability to identify promising targets early on and open science and sharing of data may help in this regard.

By observing the phenotypic effect that results from a decrease in the target protein you can confirm whether the target warrants further development. As both phenotypic and target-based drug discovery approaches each have distinct benefits and challenges, perhaps rather than being viewed as opposing drug discovery strategies, they should be seen as complimentary, which, if used together could increase the likelihood of discovering a truly novel therapeutic strategy.

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Boscha, F. Pharmacology, 82 3 , Gashaw, I. What makes a good drug target?. Drug Discovery Today, 17, SS Owens, J. Phenotypic versus Target-based Screening for Drug Discovery. Terstappen, G. Target deconvolution strategies in drug discovery. Nature Reviews Drug Discovery, 6 11 , Moffat, J. Opportunities and challenges in phenotypic drug discovery: an industry perspective.

Nature Reviews Drug Discovery, 16 8 , Croston, G. The utility of target-based discovery. Expert Opinion on Drug Discovery, 12 5 , Lindsay, M. The solubility data can assist medicinal chemists to evaluate the drug candidates without having to synthesize molecules at all. This greatly reduces the costs of molecule synthesis and time for experimental solubility measurements.

Huynh et al. This in silico model was in agreement with the experimental solubility of DTX. Simulation-based approaches are frequently used in computational permeability prediction [,]. In one study, trajectories obtained by molecular dynamic simulations have been used to obtain diffusion coefficients of permeation of drug-like molecules through the blood-brain barrier []. In silico approaches to predict drug solubility in both aqueous media and DMSO are discussed in a review [].

Human intestinal absorption of a candidate drug is of high importance because it can affect the bioavailability of a drug. There are extensions of the Rule of 5 in predicting drug-likeliness as well []. These rules are generalized rules for evaluating the drug-likeness and bioavailability of compounds. Various statistical and mathematical models have been based on these rules and their extensions. Machine learning algorithms such as neural networks have been used in the prediction of drug-likeness and bioavailability [,].

QikProp is an ADME program offered by Schrodinger that predicts pharmaceutically relevant and physically significant descriptors for small drug-like molecules []. These ADME models can then be used to predict the behavior of novel molecules. It can also be used to find molecules with similar ADME properties as active ligands of interest. FAF-Drugs2 is an ADME and toxicity filtering tool that can calculate physicochemical properties, toxic and unstable groups, and key functional components []. Even though many possible drug molecules go to experimental verification stage or even animal models, they do not reach clinical trials.

This is mostly due to the fact the drugs have poor pharmacokinetic properties and toxicity []. Thus filters for ADME properties are important for drug screening []. Computational ADME methods have advanced greatly in the last few decades and pharmaceutical companies are showing great interest in this area []. In the case where the potential drug target structure is unknown and predicting this structure using methods such as homology modeling or ab initio structure prediction is challenging or undesirable, the alternative protocol to use is Ligand-based drug design [,].

Importantly, however, this method relies on the knowledge of small molecules that bind to the target of interest. Pharmacophore modeling, molecular similarity approaches and QSAR quantitative structure—activity relationship modeling are some popular LBDD approaches []. In molecular similarity methods, the molecular fingerprint of known ligands that bind to a target is used to find molecules with similar fingerprints through screening molecular libraries []. In ligand-based pharmacophore modeling, common structural features of ligands that bind to a target are used to do the screening [].

QSAR is a computational method that models the relationship between structural features of ligands that bind to a target and the corresponding biological activity effect []. The main idea of similarity-based or fingerprint-based approaches is to select novel compounds based on chemical and physical similarity to known drugs for the target. Ligand similarity search methods are simple but effective approaches based on the theory that structurally similar molecules tend to have similar binding properties [].

These similarity measures do not take into account information about activities of known binders of the target. The final similarity score that was used comprised a 2D score and a 3D structure similarity component []. A pharmacophore is a molecular framework that defines the essential features responsible for the biological activity of a compound. When structural information about the drug target is limited or not known, pharmacophore models may be built using the structural characteristics of active ligands that bind to the target [].

When 3D information of the target structure is known this binding site information can also be used in generating pharmacophore models [].

Quantitative Methods in System-Based Drug Discovery

Pharmacophore modeling has also been used in virtual screening of drugs in large databases []. However, this molecule has never gone past clinical trials due to its low potency. This active compound was optimized using ligand-based pharmacophore modeling to develop highly potent analog SR which is a novel drug that shows to be highly potent against several cancer types [5]. Pharmacophore model construction steps can be summarized as follows:. QSAR methods are based on statistics that correlate activities of target drug interactions with various molecular descriptors.

The basis of the QSAR method is the fact that structurally similar molecules tend to show similar biological activity []. These models describe mathematically how the activity response of a target, that binds a ligand, varies with the structural features of the ligand.

QSAR is obtained by calculating the correlation between experimentally determined biological activity and various properties of small ligand binders []. QSAR relationships can be used to predict the activity of new drug molecule analogs. In order to quantify the activity of a drug molecule, several values can be used. Half maximal inhibitory concentration IC 50 and inhibition constant K i are the most commonly used measures. QSAR models, unlike the pharmacophore models, can be used to find the positive or negative effect of a particular feature of a drug molecule to its activity.

QSAR methods have been used successfully on various drug targets such as carbonic anhydrase [,] , thrombin [,] and renin []. Different machine learning techniques have also been used in constructing QSAR models []. In classical or 2D QSAR methods, the biological activity is correlated to physical and chemical properties such as electronic hydrophobic and steric features of compounds []. In more advanced 3D QSAR methods, in addition to physical and geometric features of active drug molecules, quantum chemical features are also used.

Recently QSAR models have also been developed for membrane systems []. Known drug molecule activity and descriptor data is obtained and the mathematical model of QSAR is built such that descriptors can predict the activity of each molecule. The predictive power of models are validated and used in predicting activities of novel compounds. Known drug molecule activity and descriptor d Success of a QSAR depends on the molecular descriptors selected and the ability of these models to predict biological activity. If there is not enough activity data to extract patterns, QSARs cannot perform well.

Therefore, this method requires a certain minimum amount of training data in order to build a good predictive model and it is often linked to high-throughput screening. Statistical methods have been used in linear QSAR to pick molecular descriptors that are important in predicting the biological activity. MLR multivariable linear regression can be used to find molecular descriptors that have a good correlation with the target—ligand biological activity. It is only possible to use linear regression methods if the activity descriptor relation is linear. However the relationship between biological activity and the molecular descriptors are not always linear [].

Machine learning approaches such as neural networks and support vector machine methods are used to generate QSAR models to address this issue of non-linear fitting []. Principal component analysis PCA can be used to simplify the complexity by removing the descriptors that are not independent []. Once the right set of features is identified and the QSAR is built, these models can be validated using methods such as cross validation [,].

QSAR models can be used to predict the biological activity of novel molecules by just using the molecular features. Thus these models can be used to screen a database of molecules to find potential active molecules. Some of the drugs that are on the market with the help of ligand-based drug discovery are Zolmitriptan, Norfloxacin and Losartan [8].

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Norfloxacin is a drug that is used in urinary tract infections and was developed using a QSAR model and approved by the FDA in []. Figure 9: A few drugs discovered with the help of ligand-based drug discovery tools. One difference between pharmacophore models and QSAR is that the pharmacophore model is constructed based on the necessary or essential features of an active ligand, whereas QSAR takes into account not only the essential features but also the features that affect the activity. One important structural feature used in both the pharmacophore model and in QSAR is the volume of the binding site.

It is well established that the binding pocket volume has a big influence on the biological activity. Machine learning algorithms can be trained to identify patterns in data and used to do predictions on test data sets. These algorithms are extensively applied in the field of biology and drug discovery [].

Machine learning is used in many stages in the drug discovery pipeline including in the QSAR analysis stage []. Support vector machine SVM based algorithms are commonly used and have been shown to have high predictive power. SVM are often used for classification of sets of biological data. For example, they can be used to distinguish between molecules that have high affinity for a target and those that have no affinity. Machine learning based scoring functions can also be used in structure-based drug discovery to predict target—ligand interactions and binding affinities [].

Compared to conventional scoring functions, machine learning based scoring functions have often shown comparable or even improved performance. Moreover these algorithms can be trained to distinguish active drugs from decoys that do not have known drug activity []. Artificial neural networks ANNs have been used in drug discovery as a powerful predictive tool for non-linear systems []. Docking algorithms were then used to find novel inhibitors that bind to aldose reductase.

ANN-based prediction models are also used in predicting biotoxicity of molecules as well []. In the past 10 years the identification rate of disease-associated targets has been higher than the therapeutics identification rate. With considerable rise in the number of drug targets, computational methods such as protein structure prediction methods, virtual high-throughput screening and docking methods have been used to accelerate the drug discovery process, and are routinely used in academia and in the pharmaceutical industry. These methods are well established and are now a valuable integral part of the drug discovery pipeline and have shown great promise and success.

It is cheaper and faster to computationally predict and filter large molecular databases and to select the most promising molecules to be optimized. Only the molecules predicted to have the desired biological activity will be screened in vitro. This saves money and time because the risk of committing resources on possibly unsuccessful compounds that would otherwise be tested in vitro is reduced.

Structure-based and ligand-based virtual screening methods are popular with most of the applications being directed towards enzyme targets []. Even though structure-based methods are more frequently used, ligand-based methods have led to the discovery of an impressive number of potent drugs. In SBDD knowing the three-dimensional structure of the target of interest is required. However, in some cases it is not possible to determine structures of targets using conventional experimental methods due to experimental challenges.

In the cases where experimental methods fail, computational methods become useful and potentially necessary for SBDD [23]. In the absence of an experimentally determined structure or a computationally generated model for a target of interest LBDD tools can be used. These tools require the knowledge of active drugs that bind to the target. Experimental methods usually represent proteins as static structures.

However proteins are highly dynamic in character and protein dynamics play an important role in their functions. Computational modeling of the flexible nature of proteins is of great interest and various ensemble-based methods in structure-based drug discovery have emerged []. Molecular dynamics simulations are widely used in generating target ensembles that can be subsequently used in molecular docking [].

Docking tools have been developed with different scoring functions and search algorithms. Comparative studies have been performed to evaluate these scoring functions and docking algorithms in docking pose selection and virtual screening [,,]. There is no one superior tool that works for all target—ligand systems. The quality of docking results is highly dependent on the ligand and the binding site of interest []. VHTS methods are useful to screen large small molecule repositories fast and pick a smaller number of possible drug-like molecules for testing. By reducing the number of possible molecules that need to be tested experimentally, these methods can help to greatly cut the cost associated with drug discovery process.

Studies have shown that with VHTS it is possible to identify molecules that are not observed with conventional high-throughput screening HTS experiments []. The molecules selected by both of these methods are more likely to be possible drug candidates and should be considered when selecting hits. Adverse effects in animal models or even clinical trials can be reduced by filtering drug candidates by their ADME properties in early stages. Another important fact to consider in drug safety studies is how one drug can affect the metabolic stability of another drug [].

Some drug—drug interactions DDI could lead to serious health effects; therefore, predicting these effects is important but challenging. The prescription antihistamine terfenadine and antifungal drug ketoconazole are two examples of drugs that should not be co-administered []. Terfenadine—ketoconazole drug—drug interactions results in cardiotoxicity.

Computational methods such as pharmacokinetic modeling and predicting drug—drug interactions using large DDI interaction databases are successful and are both cost and time saving as well [,]. Currently hybrid structure-based and ligand-based methods are also gaining popularity. These combined ligand-based and structure-based drug discovery methods are of interest because they can amplify the advantages of both methods and improve the protocols []. One example is the hybrid docking protocol HybridDock, which incorporates both structure-based and ligand-based methods [].

This hybrid method shows significantly improved performance in both binding pose and binding affinity prediction. CADD has had a significant impact on the discovery of various therapeutics that are currently helping treat patients. Despite the successes, CADD also faces challenges such as accurate identification and prediction of ligand binding modes and affinities [8]. One of the challenging areas in drug discovery is the phenomenon of drug polymorphism [].

Drug polymorphism occurs when a drug has different forms which are identical chemically but differ structurally. This can have a great impact on the success of a drug. Different polymorphic forms of a drug, which have different solid-state structures, can differ in solubility, stability and dissolution rates.

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Drug polymorphism can affect the bioavailability, efficacy and toxicity of a drug. One polymorphic form that is responsible for a particular drug effect may differ if a different polymorphic form of the same drug is administered. Using techniques such as spectroscopy it is possible to characterize drugs having different polymorphic forms. Protein—protein interactions PPIs pose another challenge in drug discovery.

PPIs are involved in many cellular processes and biological functions that are linked to diseases. Therefore, small molecule drugs that aim at PPIs are important in drug discovery []. It is of interest to develop therapeutics that can either disrupt or stabilize these interactions. However, it is challenging to design inhibitors that can directly interrupt PPIs. Common drug design usually targets a specific binding site on a protein of interest. However, protein—protein interacting surfaces have larger interfaces and are more exposed. Therefore their binding sites are often not well defined.

Finding the sites that can be aimed at in PPI inhibition is therefore challenging and of great importance. Through collaboration with the Drug Design Data Resource D3R , which is a project funded by the National Institutes for Health, pharmaceutical companies are able to release their previously unreleased drug discovery data to the scientific community. This project allows the scientists all over the world to use new high-quality data in improving computer-aided drug discovery and design, and also to speed up the progress. The field of CADD is continuously evolving with improvements being made in each and every area.

Some of the focus areas are scoring functions, search algorithms for molecular docking and virtual screening, optimization of hits, and assessment of ADME properties of possible drug candidates. With the current successes there is a promising future for computational methods to aid in the discovery of many more therapeutics in the future.

Helge B. Kay M. Brummond, John R. Goodell, Matthew G. Maria C. Silla and Matheus P. Twitter: BeilsteinInst. Beilstein J. Toggle navigation. Please enable Javascript and Cookies to allow this site to work correctly! Computational methods in drug discovery Sumudu P. Leelananda and Steffen Lindert. Sumudu P. Steffen Lindert. Review PDF Album. Graphical Abstract. Jump to Figure 1. Structure-based drug discovery SBDD If the three-dimensional structure of a disease-related drug target is known, the most commonly used CADD techniques are structure-based.

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Jump to Figure 3. Jump to Figure 4. Jump to Figure 5. Jump to Figure 6. Jump to Figure 7. Jump to Figure 8. Jump to Figure 9. Poverty , 5, No. Physiology , 25, — Science , , — Homology Modeling. Ab Initio Protein Structure Prediction. Science , Suppl. Curr Protoc. Bioinformatics; Unit 5. Structure , 21, — Nature , , 86— NMR , 18, — Structure , 20, — Structure , 17, — Structure , 16, — D1 , D—D Genomics , 12, — Bioinformatics , 21, — Web Server issue , W—W Tetrahedron , 64, — Neuron , 60, — Nature , , — B , , — Biopolymers , 68, 47— A , , — Millisecond-scale molecular dynamics simulations on Anton.

Discovery , 4, No. Methods , 44, — Molecules , 5, — Discovery , 3, — Methods , 45, 65— Reference Go to reference CO;2-O Go to reference References , References 93, References Reference 4. Go to references CO;2-F Go to reference References 55,64, References 82, References 79, References 73, LigPrep, 2. Reference 8. Reference 3. References 6,, CO;2-A Go to reference Reference 5.

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