Frontiers in Drug Design and Discovery

For more than a decade, mass spectrometry (MS) has played an important role in absorption, distribution, metabolism, excretion and toxicology (ADMET) studies for drug discovery to help convert lead compounds into drug candidates. Drug discovery efforts have been focused on identifying drug metabolism and pharmacokinetic (DMPK) issues at the earliest possible stage to reduce attrition rate of drug candidates throughout the drug development process by applying cutting edge MS-based techniques. These emerging techniques have proven to be extremely valuable to accelerate the lead optimization and characterization processes by eliminating potentially unpromising candidates. In this article, the current MS-based approaches and their future perspectives in supporting exploratory DMPK studies including in vitro and in vivo pharmacokinetic profiling, physical property, metabolite identification and molecular imaging tests are reviewed.

Glutathione transferases (GSTs) are enzymes involved in cellular detoxification by catalysing the nucleophilic attack of glutathione (GSH) on the electrophilic centre of a number of electrophilic compounds of both endogenous and exogenous origins. This conjugation reaction usually makes the electrophilic substrates more water soluble and, thereby, facilitates their excretion from the body. Determination of metabolic properties of a new chemical entity (NCE) is one of the most important steps during the drug discovery and development process. Nowadays, in vitro methods are used for early estimation and prediction of in vivo metabolism of NCEs. In this review detailed descriptions are given of several biotransformation reactions catalyzed by GSTs that can be used at very early phases of drug development, thereby enabling unsuitable candidates to be eliminated from consideration much earlier in the drug discovery process. Knowledge of the structure-function relationships in classes of compounds that are substrates for GSTs enables the design of molecules that can be stable, or labile which has potential applications in drug and prodrug design.

Considering that pharmacokinetic-pharmacodynamic (PK-PD) modeling describes the relationship between tissue concentrations of drugs and their corresponding pharmacological response, an important issue of PK-PD studies is the availability of powerful sampling techniques that allow measurement of tissue concentrations of drugs at multiple time points. Traditional sampling techniques, including biopsy, blood and saliva sampling, and skin blister sampling, have several limitations for drug monitoring during PK-PD studies, considering that these techniques did not allow the measurement of drug concentrations at the site of action. In the last decades, new sampling techniques, including membrane based techniques (microdialysis and ultrafiltration) and imaging techniques (positron emission tomography and magnetic resonance spectroscopy), have been available for measurement of drug concentration at the target site. The possibility of simultaneous monitoring of target site concentrations of drugs and their pharmacological effect with these new sampling techniques have significantly improves current knowledge of PK-PD modeling. In addition, membrane based techniques also allow simultaneous monitoring of endogenous compounds and therefore permit the study of the relationship between drug target site concentrations and their effect on biochemical markers, making these techniques highly useful for PK-PD modeling studies. The aim of this chapter is to describe the principles of membrane based techniques and imaging techniques, and their applicability for drug monitoring in PK-PD modeling.

High levels of inflammatory cytokines and adhesion molecules are associated with many inflammatory disorders [e.g. rheumatoid arthritis, inflammatory bowel disease and lupus] as well as metabolic and cardiovascular diseases including diabetes and obesity. Examples of such markers include tumor necrosis factor [TNFα], interleukins [IL-1, IL-6, IL-8 and IL-18], vascular cell adhesion molecules and markers of macrophage inflammation [e.g. MMPs]. In many preclinical disease models, levels of these markers are significantly elevated relative to normal animals. Modulation of these biomarkers with pharmaceutical agents in preclinical and clinical studies can be effectively used for concept validation, effective dose selection, and establishing good pharmacokinetics/pharcodynamics correlation. On the other hand, elevation of these markers in normal animals, following treatment with an agent, could indicate safety concerns leading to potential tissue damage. Monitoring of inflammatory markers in normal animals can be diagnostic and of high value in evaluating safety or efficacy of new molecules. The levels of biomarkers can be monitored either by high throughput microarrays/proteomics or by specific ELISA based assays. Since many of the biomarkers appear in systemic circulation, these can be monitored in blood/plasma without interference with tissues. This makes the approach particularly attractive for clinical studies. An overview of the biomarkers, potential applications and case histories linking biomarkers to PK/PD correlation from preclinical and clinical studies are discussed.

Drug interactions can cause severe side effects and lead to early termination of drug development, refusal of drug approval, prescribing restrictions or drug withdrawal from the market. Of drugs used to treat humans, cytotoxic anti-neoplastic drugs have a particularly strong action. Furthermore, they have a complex pharmacological profile, a narrow therapeutic window, and a steep dose-toxicity curve, and are associated with considerable inter- and intrapatient pharmacokinetic and pharmacodynamic differences. The recommended dose is usually close to the maximally tolerated dose in order to achieve the maximum therapeutic effect. Thus, some adverse effects are usually inevitable, so these drugs are approved for usage based on a clinical risk to benefit ratio. Therefore, drug interactions affecting the pharmacokinetics of anti-neoplastic drugs are of particular concern. Any physicians treating oncology patients must understand the pharmacokinetic behavior (absorption, distribution, metabolism, excretion, etc.) of a drug, as well as the factors affecting its pharmacokinetic behavior, for example the effects of concomitantly administered drugs, and hepatic and renal function. Medical oncologists must have expertise in achieving a good balance between safety and efficacy in medical treatment, with a proper knowledge of supportive care and an understanding of pharmacokinetics, pharmacodynamics and pharmacogenomics. We summarize the drug interactions that are important in day-to-day oncology practice. We cover pharmaceutical interactions as well as the interactions at the levels of absorption, distribution, metabolism and excretion. This review is the one of the most comprehensive to date in the field of clinical oncology, where the level of understanding of drug interactions can directly affect patient management.

Many factors affect an individual's response to a drug, and large inter- ethnic, intra-ethnic, and even intra-individual variations exist. These variations may affect both the therapeutic response to a drug, or the side effects that the patient experiences. Since anti-neoplastic drugs often have a very narrow therapeutic range, it is very desirable to be able to predict these variations in response or to ensure that these variations are as small as possible. It has recently become possible to predict some extreme responses, such as severe side effects, using pharmacogenomic approaches; for example, the uridine diphosphate-glucuronosyltransferase (UGT) 1A1 genetic polymorphism is a predictor of irinotecan toxicity. Further, adding pharmacokinetic and pharmacodynamic information may increase the accuracy of response prediction. Both severe toxicity and clinical benefit can be predicted using a combination of pharmacogenomic and pharmacokinetic information. For example, the clinical benefit obtained from adjuvant treatment with tamoxifen is reduced in patients who have either a particular Cytochrome P450 (CYP) 2D6 genetic polymorphism or who are taking paroxetine, a strong inhibitor of CYP2D6. It is possible to monitor pharmacodynamic parameters, such as serum estrogen levels, as a measure of the therapeutic effect of aromatase inhibitors. In this review, we summarize current knowledge in the field of pharmacogenomics as it relates to breast cancer, focusing particularly on clinical data.

Advanced human tissue equivalents are an emerging drug discovery tool that aims at minimizing costly candidate attrition in later stages of preclinical and clinical development. 3-D cellular tissue models amenable to screening in 96-well plate format and drug monitoring in real time provide more accurate compound screening in a physiologically relevant context, not achievable in traditional two dimensional, single cell type-based assays. Currently, equivalents that represent the healthy or pathological physiology of human tissues including skin, vasculature, lung, prostate, and various malignant tumors are used for rapid activity screening, toxicity profiling, and pharmacokinetic characterization of compound libraries. Human skin equivalents with intact stratum corneum reconstructed in vitro from matrix-embedded dermal fibroblasts and epidermal primary keratinocytes closely resemble the complex architecture and functional complexity of skin. Using human skin equivalents, delivery of novel topical agents for photoprotection has been studied, and toxicity and activity profiling of skin care products and FDA-approved drugs including sunscreens has been performed. Importantly, human skin equivalents are better predictors of drug activity than available animal models as mouse and guinea pig skin do not reflect the architecture of human skin in terms of physico-optical properties such as light reflectance and scattering, epidermal thickness, cellularity, and biochemical composition. Recently, cellular composition of advanced commercial skin reconstructs has been further optimized by incorporation of melanogenic melanocytes and immunomodulatory dendritic (Langerhans) cells in order to assess drug modulation of cutaneous pigmentation, inflammation, photo-immunosuppression, and photo-carcinogenesis. Continuous progress in skin equivalent engineering will ensure the expanding role of skin equivalents in disease model-based assays for rapid identification and development of novel cutaneous therapeutics.

Skin is still the desirable route for the delivery of drug substances into the human body. Transdermal drug delivery offers many advantages over the conventional oral route of application, such as the elimination of hepatic first-pass effect, reduced side effects, constant concentration of a drug in the blood. Human intact skin is normally permeable for molecules with log P in the range of 1-3, smaller than 500 Da and present in a unionized form. Usually, obtained fluxes of drug substances are too low for the induction of systemic therapeutic effects. It is caused by the specific structure and composition of the outer layer of the skin - the stratum corneum. Closely packed, built as “brick” (corneocytes) and “mortar” (lipid bilayers), the stratum corneum is the most important limiter for transdermal drug delivery. Molecules that permeated the stratum corneum are easily taken up by capillary vessels present in the deeper skin layers. This chapter presents different methods used for skin permeation enhancement. Various drug forms and carriers, chemical permeation enhancers, electrically supported methods and devices, and the stratum corneum bypassing or removing methods are described, and the recent achievements in the field and possible practical use in market products are discussed. The special subchapters are dedicated to the skin disposition of one of the most often used penetration enhancers - terpenes, and the use of cyclodextrins in formulations applied onto the skin.

Quantification of drugs within the skin is essential for topical and transdermal delivery research. Over the last two decades, horizontal sectioning, consisting of tape stripping throughout the stratum corneum, has become one of the traditional investigative techniques. Tape stripping of human stratum corneum is widely used as a method for studying the kinetics and penetration depth of drugs.

The Food and Drug Administration released a draft guidance proposing a Dermatopharmacokinetic method for evaluating bioavailability and/or bioequivalence of topical dermatological drug products. As specified in this document, the method measures topically applied drug levels in the outermost layer of the skin, the stratum corneum, as a function of time post-application and postremoval of the formulation, so as to generate a stratum corneum concentration versus time profile. The stratum corneum is collected by successive application and removal of adhesive tape providing a minimally invasive technique by which the drug's concentration in the skin can be determined. The Dermatopharmacokinetic method assumes that: (i) in normal circumstances, the stratum corneum is the rate-determining barrier to percutaneous absorption, (ii) the stratum corneum concentration of drug is directly related to that which diffuses into the underlying viable epidermis, and (iii) Stratum corneum drug levels are more useful and relevant for assessing local, dermatological efficacy than plasma concentrations.

This paper shows the applications of the tape stripping technique to evaluate drug penetration through the skin as well as stratum corneum composition and physiology, underlining its versatile application in the area of topical and transdermal drugs.

In recent years Attention Deficit Hyperactivity Disorder (ADHD) has been the focus of growing interest, and different drugs have been introduced for its treatment. Thus, there is a range of medication for ADHD, but new formulations are necessary for more individualized therapy. The choice will depend upon the circumstances and detailed assessment. A new extendedrelease formulation of methylphenidate (Medikinet®) has increased the drugdelivery treatment options for ADHD. Medikinet® combines the advantages of immediate-release (IR) and extended-release (ER) formulations of methylphenidate, with rapid onset and prolonged duration of action (7-8 h), in a single dose intended for once-daily administration. The concentration-time profile is achieved through the particular formulation of Medikinet®, whose hardgelatine capsule contains 50% enteric-coated and 50% uncoated pellets, providing both a first, immediate release and a second, delayed release. The coated pellets only dissolve at a pH < 5.5 and release the active drug in a sustained way into the intestine. There is no difference in the bioavailability of the IR/ER product when administration follows a normal or high-calorie breakfast. Medikinet® also shows a bioavailability comparable to that of the b.i.d. 10 mg immediate release regime, as well as a high level of efficacy and good tolerability. In this review, we describe the pharmacokinetics of Medikinet® and compare its characteristics with those of other formulations used for treating ADHD.

Chronic pain requires long-term therapy and controlled-release opioids are widely used for its management. One of the major causes of suboptimal therapy outcomes is poor adherence to prescribed therapy. Better adherence to treatment can be obtained by reducing dosing frequency. Oncedaily administrations were shown to be effective and well accepted by patients. The osmotic-controlled release oral delivery system (OROS®) is an advanced drug delivery technology that uses osmotic pressure as the driving force to deliver pharmacotherapy in many therapeutic areas. Over the past decades, different OROS® osmotic dosage forms have been studied to optimize extendedrelease oral administration by controlling the rate of drug release, providing different delivery profiles. OROS® hydromorphone has been recently introduced in clinical practice for treating patients with chronic cancer and noncancer pain. OROS® hydromorphone ensures a constant, monophasic delivery of hydromorphone over a 24-hour period. The pharmacokinetic profile of OROS® hydromorphone is minimally affected by food and alcohol. Doseconversion studies showed that patients with chronic pain could be switched easily from previous opioid therapy to OROS® hydromorphone, without loss of pain control. These studies support the clinical utility of the 5:1 ratio used for the conversion of oral morphine to oral OROS® hydromorphone. Oncedaily OROS® hydromorphone was shown to be effective in patients with chronic low back pain, and to provide similar pain relief to that of ER oxycodone in patients with moderate to severe osteoarthritis pain. OROS® products can result in an improved safety profile, more stable drug concentrations, uniform drug effects, and reduced dosing frequency.

Colloidal delivery systems such as oil-in-water emulsions, liposomes, microparticles and nanoparticles, show great potential as a means of delivering a drug to its site of action efficiently, thereby minimizing any unwanted toxic effects. In this point of view, membrane emulsification has received increasing attention over the last 10 years. In the membrane emulsification process, a liquid phase is pressed through the membrane pores to form droplets at the permeate side of a membrane; the droplets are then carried away by a continuous phase flowing across the membrane surface. The purpose of the present paper is to provide a state of the art on membrane processes to prepare drug delivery systems. The following are included: principles of membrane emulsification, colloidal delivery systems, reduction of adverse affects, active principles, encapsulation efficiency, and drug release properties.

During the past decade, the pharmaceutical industry has invested considerably in technologies that have the potential to increase throughput in discovery projects. With the increase in the numbers of molecules synthesized in a typical drug discovery program, as well as the large amount of information utilized in the selection of a drug candidate, it is very useful and necessary ADME and pharmacokinetic information during the discovery process. Over the past decade, many in vitro, and even in vivo, ADME/PK screening have been developed and routinely deployed to generate this information in support of drug discovery efforts. In the past few years, alternative methods as in silico methods have been published. The great challenge for in silico methods is generation of models that correlate more closely with in vivo systems. This review attempts to summarize the in silico approaches taking into account the (i) ways of evaluating a molecule for ADME properties (type of descriptor) and (ii) the employed method for prediction of ADME properties. Progress in this area will be discussed, focussing on oral absorption, blood-brain barrier and metabolism, and some aspects on excretion will be also briefly commented.

A large number of compounds in the development stage got failure due to the unfavourable ADMET (absorption, distribution, metabolism, excretion and toxicity) profiles. The utilities of ADMET properties are becoming progressively more imperative in the drug discovery processes, assortment, development and promotion processes. In recent years several review papers have been published about the possibilities of the prediction or the ADMET properties using different structural features of the molecules, i.e., molecular descriptors, and utilizing multiple approaches. One of the most important approaches is QSAR modelling of the data derived from their activity profiles and their different structural features (i.e., quantitative molecular descriptors). More and more efforts are put to the field of ADMET predictions. This chapter will critically assess some of the most important and recently reported topics for the effective in silico predictions of the ADMET properties of the potential drug candidates based on QSAR modelling approaches.

Quantitative structure-property relationship (QSPR) models have proven to be an effective approach for increasing the efficiency of small molecule drug discovery and development processes. Despite their importance to drug discovery, difficulties remain in the appropriate selection and weighting of descriptors, determination of appropriate descriptor combinations, and optimization strategies that can increase the value of QSPR models. Here we review the utility of some of the more popular applications of computational intelligence to QSPR modeling including: artificial neural networks, fuzzy logic, and evolutionary computing.

In pharmaceutical industry, in addition to high potency, good absorption, distribution, metabolism and excretion (ADME) profiles of compounds are needed for drug development. Data modeling of ADME model is a crucial step for efficient drug design. However, we have to avoid so called a situation, the black box, which might be difficult for chemical interpretation. The right balance between precision and interpretation is required for practical drug design.

We review the related articles to focus several ADME modeling techniques. As regression, multiple linear regressions (MLR), partial least squares (PLS), artificial neural networks (ANN), support vector machines (SVM) are picked up and their algorithms and the representative applications are introduced. We pay attention to rule mining methods for chemical interpretation. As rule mining, rough set theory (RST) is shown as an example. Visualization is a classical but never neglected technique for easily understanding the overall behaviors of huge compounds. We especially spend more pages about kohonen neural networks (KNN) and decision trees (DT) as the representative methods. Furthermore, web application for chemists is another important aspect for practical drug design. Recent trend about this topic is shown in two industry cases. As conclusion, we will show future direction concerning in silico ADME prediction.

Virtual reality interfaces and haptics are rapidly becoming a powerful technology to enable researchers to interactively manipulate and evaluate potential drug molecules in an immersive virtual environment to accelerate the drug design process. Virtual reality refers to a computer-generated and interactive three-dimensional environment that immerses people into a virtual world while haptic devices are electromechanical devices that exert forces on users giving the illusion of touching something in the simulated environment. As molecular forces play a major role in determining the successful docking of drug molecules, virtual reality and haptics can provide researchers with invaluable human-computer interface tools for visualizing, manipulating, and “feeling” complex molecular systems in real time. The force feedback provided by haptic devices can direct researchers towards favorable drug molecule positions and orientations increasing the understanding of key forces during molecular interactions and enabling new kinds of drug design exploration. However, the main difficulty of modeling molecular systems through virtual reality and haptics is that visualization models and simulations need to be processed rapidly to satisfy the update requirements needed for real-time visualization and sense of touch. Any time delay between a user action and the corresponding update of the virtual object can lead to unrealistic visualization, unstable force response, and simulation sickness. This paper reviews some of the research advances for addressing these computational challenges ranging from new graphical representations of molecules for effective haptic force feedback calculation to virtual reality algorithms and devices for modeling complex molecular systems in a real-time virtual environment.