2New Methods in Synthesis and Development for Pharmaceuticals

Annual sales in the pharmaceutical industry have been growing in the double-digit range for many years. These numbers are expected to decrease in the future because of patent expirations on major products, pressure to reduce healthcare expenditures, larger spending on sales and marketing, and the increased cost of research and development. Because the market for the leading therapeutic classes of drugs is over $350 billion per year, there is considerable incentive to pursue opportunities for new drug discovery. These opportunities must be addressed, however, in the face of fierce competition in an industry that is consolidating and experiencing considerable pressure on pricing. These factors will require intelligent and efficient management of the significant risks and costs associated with pharmaceutical research and development.

Finding safe, effective medicines has always been the goal of the pharmaceutical industry. Better understanding of the biochemical mechanisms for diseases has improved the scientific basis for drug discovery. It is anticipated that genomics, proteomics, and bioinformatics will further enhance the drug discovery process by providing a more advanced understanding of disease processes and revealing new opportunities for successful intervention with drugs (see Sidebar 2.1). These new tools, along with others such as high-throughput screening, combinatorial chemistry, and micro array technology have required significant capital and human resource investments before the capture of clear value in productivity. Subsequently, costs and risk in drug discovery increase before it can be established that the new tools and technologies improve the efficiency of the process. This is a challenge for the industry because cost effectiveness and affordability of product are vital issues in drug discovery and development.

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Sidebar 2.1

The Trend toward Personalized Medicine. Excerpt from “Bioprocessing”, James R. Swartz, Stanford University The genomics revolution is working toward personalized medicine, requiring precise diagnostics and rapid, inexpensive drug production. (more...)

The pharmaceutical industry of today evolved largely from the chemical industry. As these roots would suggest, chemistry was a key component of early drug discoveries that were focused on pain management and the treatment of inflammation and infectious diseases. Advances in science related to the structure and function of DNA, as well as powerful methods for manipulating DNA and making proteins, has led to a more balanced partnership for drug discovery between chemistry and biology. Understanding the structure and function of these biopolymers has provided a common language for the partnership to use for strategic and tactical purposes. The result was a commonly used process for drug discovery. This process focused initially on four key points: (1) selection of a therapeutic target, (2) linkage of the chosen target to a defined biological mechanism of drug action, (3) discovery of a lead compound that worked by this mechanism, and (4) optimization of the lead for potency and selectivity of the biological activity. Pursuit of this scheme revealed the importance of including other considerations in the optimization process at an early time point. Thus, drug absorption, distribution, and metabolism (ADMET) and certain safety studies were incorporated into the selection process for potential drug development candidates. Questions related to “what the drug does to the body” and “what the body does to the drug” are addressed in this scheme. While these additional studies add time and expense to the discovery phase of the process, justification for this comes from higher-quality compounds being entered into the more expensive development phase of the overall process that leads to a new drug.

Selection of a therapeutic target based on unmet or undermet clinical need is an important early step in drug discovery. Increased use of outcome studies to establish the therapeutic value of new medicines has raised target choice to a new level of sophistication. Third-party players may require a study of this type for reimbursement. Because outcome studies can be difficult to design and expensive to execute, it is important to carefully research this issue as part of the initial project proposal.


The explosion of information regarding biological pathways, such as gene and protein expression, modulation and regulation, and cell signaling, raises the challenge of target selection to critical importance, given the immense effort required to discover and develop compounds. Once the therapeutic target has been selected, linking the target with a specific biological mechanism for drug action provides focus for the discovery. To accomplish this goal it is necessary to identify the relevant biological assays. An example is provided by the work that led to the discovery and development of HIV protease inhibitors for treatment of HIV infection. This viral enzyme is required for replication. A cell-free assay in which enzyme inhibition could be measured was used to define the biological mechanism of drug action. Compounds that were active in the enzyme assay were then evaluated in cell culture systems that were subjected to HIV infection. Compounds that act by this mechanism and can achieve an adequate concentration in these cells would be expected to inhibit viral replication in a concentration-dependent manner. Thus, data from these two assays provided a useful coupling between the mechanism of drug action and the expected response. Medicinal chemists used data from these assays to guide progress from early lead compounds to clinically effective drugs.


Leads for drug discovery are frequently identified by screening collections of compounds available from synthesis or by isolation from natural sources. In that these collections or libraries of compounds may be large (> 100,000), high-throughput screening methods and equipment have been developed to facilitate the work. In certain cases it has been possible to generate a lead by modifying the structure of a substrate involved in the biological mechanism that is being studied. Medicinal chemists who use synthetic organic chemistry and a variety of design tools and techniques pursue optimization of lead molecules for therapeutic properties. The two central issues faced by the medicinal chemist are “what to make” and “how to make it.” The how-to-make knowledge is derived largely from synthetic organic chemistry. Because many drugs have at least one stereo center, recent major advances in synthetic methods addressing this issue have been of particular importance to medicinal chemistry. Parallel methods for rapidly making analogs of leads have been useful in some cases. Multiple factors are involved in deciding what to make. In as much as most drug molecules interact noncovalently with their macromolecular targets, steric, electronic and solvation factors make important contributions to the interaction energy. Design of biologically active molecules is not an exact science. Nonetheless, structure activity relationships derived from laboratory experiments and modeling data frequently contribute to the decisions about which drug to pursue. More recently, information obtained from NMR and X-ray structures of target macromolecules with and without complexed ligands has aided the design process.

While design of drug-like molecules for target affinity and selectivity is important, these molecules must also be optimized for pharmacokinetic, metabolic, physical, and toxicological properties. As a result, p450 metabolic profiling, cassette dosing in animals, cellular toxicity measurements, and the assessment of protein binding and solubility properties have become routine in the ranking of candidate compounds. The inclusion of these studies in the early phase of drug discovery has improved the quality of compounds selected for further development work. Because of their value, these data have rapidly become a significant part of the information base used by medicinal chemists to recommend compounds for development.


Focusing on the mechanism of drug action has facilitated the discovery process. Angiotensin converting enzyme (ACE) inhibitors and angiotensin-II receptor antagonists have greatly improved therapy for the treatment of hypertension. Better control of cholesterol biosynthesis through the use of HMG-CoA reductase inhibitors has reduced the incidence of coronary heart disease by more than one-third. Bone resorption inhibitors have provided effective therapy for the treatment of osteoporosis. Leukotriene receptor antagonists have improved the quality of life for patients with asthma. Serotonin agonists with receptor subtype specificity have provided effective treatment for migraine headache. Improved therapy for depression and schizophrenia also has been derived from agents that have receptor subtype profiles that differ from earlier drugs of these types. The discovery of HIV protease inhibitors and non-nucleoside reverse transcriptase inhibitors has dramatically improved prospects for patients infected with HIV. While the therapeutic advances of the last quarter-century are impressive, many opportunities and challenges remain. Better drugs are needed to treat cancer, dementia, obesity, diabetes, and infectious diseases. As this short and certainly not all-inclusive list would suggest, there is no shortage of opportunities for new drug discovery.

Organizational structures and relationships that will facilitate teamwork and open sharing of information must be developed and used in order to achieve success in the complex world of drug discovery. The workforce must be able to function as an interdisciplinary team, consisting of chemists, biologists, and scientists who specialize in molecular modeling, computational analysis, structure determination, drug metabolism, pharmaceutics, safety assessment, and all aspects of informatics. Because there are many tools that the team uses, such as high-throughput screening, combinatorial chemistry, genomics, and proteomics, produce large amounts of data, the team must have access to the resources needed to process this information. Open access to all information is important to encourage boundary crossing in the search for innovative solutions in each drug discovery project.

Structural analysis of target macromolecules using protein X-ray crystallography and NMR spectroscopy has already had a positive impact on drug design. Powerful computational programs and modeling techniques have enhanced the utility of these methods. It is likely that this trend will continue as new science evolves. Mass spectrometry, particularly in the fields of bioavailability and metabolism, has been key to rapidly obtaining information that is very useful in the candidate optimization process. While the promise of proteomics, genomics, and bioinformatics is yet to be realized, the potential of this new science to significantly facilitate drug discovery is real. The continuing advances of synthetic organic and analytical chemistry are also important to the pharmaceutical industry. Advances in parallel synthesis have the potential to rapidly expand the diversity of compounds available for study as new drugs. New chemistry that makes production of drugs more efficient has obvious commercial value. Continuing investment in all of the science that supports the advancement of knowledge at the interface between chemistry and biology is critical to achieving the full value of what we have already learned.


Research in tissue engineering has focused on developing nonimmunogenic materials to serve as scaffolds for regeneration of damaged tissue. This technology is now being applied to generate skin for severe burn victims to decrease the time required for healing and in cases where the damaged area is too large to cover with normal grafts of skin from another part of the patient’s body. One relatively low-cost approach uses an “artificial skin” to cover the burned area. The need for skin grafts and scarring is greatly reduced. Another approach uses “living skin,” a synthetic matrix with cells in the matrix, but the current cost of this material renders it impractical and cannot yet compete with approaches that do not involve the external use of cells. There are many potential applications of the technology that will require the development of new polymer matrixes with superior properties that will be absorbed or encourage adhesion of the appropriate cells and permit the development of blood vessels for oxygen transport.

Research is underway to develop materials for synthetic bone grafts. Patients with osteosarcoma often require removal of large sections of bone. Currently the only option for replacement is cadaver bone. These grafts carry the potential of disease transmission, require an available source of replacement bone, heal slowly, and are weaker than the bone that was replaced. A totally synthetic scaffold for growth of new bone will need to interact with cells in the body in a manner that attracts those cells required for healing to the wound site (e.g., the cells for depositing bone and those for forming the blood vessels needed to carry oxygen to the new tissue). This might be accomplished by designing new materials that interact with adhesion receptors on cells and the development of drugs that promote cell migration and proliferation. The set of molecular tools available is limited at this point, and additional work is needed to identify and characterize new receptors and molecules that stimulate cell migration and growth. The ligands that interact directly with cell surface adhesion receptors must be clustered to achieve their maximum effect. New synthetic procedures are needed to produce biocompatible polymers for which the concentration and presentation of ligands for adhesion of specific types of cells can be precisely controlled.

Polymer scaffolds can be used to grow bone and cartilage at the present time. One of the visions in the field of tissue engineering, which is well beyond the capabilities of current technology, is to be able to grow organs such as a kidney, heart, or liver on polymer templates. Fully developed organs are large complex structures with a complex vascular network to deliver oxygen and nutrients. Early experiments have highlighted problems associated with supplying oxygen to cells as newly growing tissue becomes more than a few microns thick.

A more tractable application of the technology for growing heart, liver, kidney, or lung tissue may lie in the development of “tissue chips” for drug development. For example, hepatitis C is the leading cause of liver transplants in the Western world. Attempts to develop new drugs for hepatitis C have been frustrating because the virus infects only humans and chimpanzees and efforts to propagate the virus outside animals have been unsuccessful. In a related vein, liver toxicity from drugs such as acetaminophen or consumption of poisonous mushrooms can result in death. The mechanisms that lead to necrosis and death are just now being elucidated in mice. Related studies cannot be done in humans, and an understanding of these diseases is being hampered by the lack of good models for how humans, not mice, respond to infection, or to the chronic or acute insults that result in liver damage. Similar problems are encountered with other organs.

The development of tissue chips comprising polymer-supported human cells that retain the functions normally associated with intact organs such as the liver would allow drug development to proceed with human tissue rather than resorting to animal models. Several advantages of such a development are immediately apparent. For example, research related to drug development and toxicity assessments would not require the heavy reliance on the current practice of test animals. Ultimately, costs for drug development could be lowered, the effects of drugs on specific human tissues could be readily assessed, and ethical concerns about the use of animals in drug screening would be eliminated. In any event, the technological problems to be solved are immense. A liver cell only remains a liver cell when it is in constant contact with its neighboring hepatic cells. Without the constant signals that cells get from their neighbors, they loose their sense of place and the related behavior they exhibit in intact tissue. One possible approach is to perfuse matrix-supported cells with the appropriate signaling molecules. How closely their properties mimic those of cells in an organ could be assessed by transcriptional profiling. The first step would involve chips consisting of a single cell type, but normal tissue often contains several different cell types and ultimately one would want to construct complex matrixes containing all the cells found in the tissue in a proper spatial arrangement.

Several hurdles must be overcome to develop this technology. A new generation of three-dimensional materials must be synthesized that permit different cell types to bind to specific regions of the support with high spatial selectivity. Small molecules that support the signaling between cells typically found in organs must be identified and synthesized. Manufacturing techniques must be developed to make the technology cost effective. The scientists and engineers who develop this technology must have a firm base in chemistry and chemical engineering and be broadly trained so they understand the special challenges posed by working with tissue. Most undergraduate and many graduate programs are not designed for the breadth of exposure needed to tie together such different fields while retaining the in-depth training in a subdiscipline. Thus, the curricula offered by colleges and universities will also need attention.


More than ever innovation requires the sharing of information across novel technologies, chemistry efforts, and biological fields – information that becomes fragmented when spread across academic labs and small biotech companies. Dealing with fragmentation of scientific knowledge is critical for future successes in the fields of health and medicine. In addition to keeping abreast of new insights, access has become a challenge. One solution has been to place information in the public domain (although protecting intellectual property often delays disclosure or constrains use); another has been to establish cross-company and -university alliances. The need for biotech alliances with large pharmaceutical companies is acknowledged by small private companies, both for the shared learning and financial support that large partners can provide. From the large pharmaceutical perspective, “enabling technologies” have been fair game for licensing-in for many years. A more recent revelation is that alliances of small biotech companies and universities are equally important to bring chemical and biological innovation into large pharmaceutical companies. In a similar vein, collaborations across small biotech companies and universities may become much more the norm for cross-discipline integration. Current alliance structures are not efficient; new approaches are needed.