Chemical Synthesis Sequence

Now I would like to turn to some of the issues of operations within the manufacturing process itself and speak to certain process controls that are expected. In a chemical synthesis sequence, as I mentioned above, intermediates will need to be fully characterized. That characterization will then lead to a set of specifications for the intermediate, that is, its level of purity, its form, etc. Test procedures that demonstrate that the intermediate meets specifications must be established. Some intermediates are deemed to be more important than others and are given specific designation, such as pivotal, key, and final intermediates. In those cases, it is necessary to demonstrate that the specific and appropriate structure is obtained from the chemical reaction and that the yield of the intermediate is documented and meets the expected yield to demonstrate process reproducibility and control. Purity of the substance is to be appropriately documented. And, finally, in reactions which produce pivotal, key, and final intermediates, side products or undesirable impurities are identified and their concentrations measured and reduced by appropriate purification procedures so that the intermediate meets in-process specifications. Thus, those important intermediates become focuses of the process to demonstrate that the process is "under control" and functioning in a reproducible and expected manner. All of these activities ultimately are designed to lead to the production of the actual active ingredient which is referred to then as a "bulk pharmaceutical agent." That final product will need to be completely characterized which then will document that it meets a set of specifications ("Final Product Specifications") for qualification as suitable for pharmaceutical use. 

In the human cell there are 23 pairs of chromosomes containing approximately 3000 million base pairs of DNA. Short sequences of DNA, perhaps with as few as 20 nucleotide units and sometimes radiolabeled, can be obtained either by chemical synthesis (gene machine) or from cloning. These short sequences can be used to probe for a complementary sequence by looking for the position to which they bind to any DNA sample under investigation, from blood for example. Such probes can detect as little as 100 fg of DNA and are the basis of forensic genetic fingerprinting tests. 

Early diffraction photographs of such DNA fibers taken by Rosalind Franklin and Maurice Wilkins in London and interpreted by James Watson and Francis Crick in Cambridge revealed two types of DNA structures A-DNA and B-DNA. The B-DNA form is obtained when DNA is fully hydrated as it is in vivo. A-DNA is obtained under dehydrated nonphysiological conditions. Improvements in the methods for the chemical synthesis of DNA have recently made it possible to study crystals of short DNA molecules of any selected sequence. These studies have essentially confirmed the refined fiber diffraction models for A- and B-DNA and in addition have given details of small structural variations for different DNA sequences. Furthermore, a new structural form of DNA, called Z-DNA, has been discovered. 

Antithetic Analysis. (Synonymous with Retrosynthetic Analysis) A problem-solving technique for transforming the structure of a synthetic target molecule to a sequence of progressively simpler structures along a pathway which ultimately leads to simple or commercially available starting materials for a chemical synthesis. 

A number of reactions of amino acids have become important in recent years because they are essential to the degradation, sequencing, and chemical synthesis of peptides and proteins. These reactions are discussed in Chapter 5. 

The large-scale reproducible manufacture of minute, electronically-stable, single-crystal transistor junctions is a triumph of the elegant techniques of solid-state chemical synthesis. The sequence of steps is illustrated in diagrams (i)-(v). 

In processes involving whole cells the required product can often be formed in a single step, although the cells essentially carry out a multi-step synthesis. This means that only a single product purification is necessary. Conversely, in chemical synthesis of compounds, each step in the synthesis is usually carried out separately. Thus the product of one reaction must often be purified before it can be used in the next step in the synthetic sequence. This multi-step approach is expensive, time consuming and can require a complex process plant to handle the individual steps on an industrial scale. 

Figure 1.1 shows that the stability sequence revealed by chemical reactions and chemical synthesis corresponds to thermodynamic stabilities. An explanation requires a theory that will explain both. To get it we apply the theory of atomic spectra [9]. The energy of the 4f electrons in an ion with the configuration [Xe]4P, F(4P), can be written [nU+E Q-p(4f )] where U, a negative quantity, is the energy of each 4f electron in the field of the positively charged xenon core, and Frep(4P) represents the repulsion between the n 4f electrons. In Table 1.1, rep(4P) is expressed as a function of the Racah parameters and E. The... 

It is now known that each codon consists of a sequence of three nucleotides ie, it is a triplet code (see Table 38—1). The deciphering of the genetic code depended heavily on the chemical synthesis of nucleotide polymers, particularly triplets in repeated sequence. 

The automated chemical synthesis of moderately long oligonucleotides (about 100 nucleotides) of precise sequence is now a routine laboratory procedure. Each synthetic cycle takes but a few minutes, so an entire molecule can be made by synthesizing relatively short segments that can then be ligated to one another. Oligonucleotides are now indispensable for DNA se-... 

Figure 2 Comparison of cloning and expression methods. In the conventional strategy (left), dehydrogenase genes obtained by PCR amplification of the original source DNAs are cloned into overexpression plasmids and verified by sequencing. Those with the desired structure are individually transformed into suitable host strains and the proteins are obtained, either as crude extracts or as purified samples. In the proposed streamlined approach (right), full-length dehydrogenase genes obtained by chemical synthesis are used directly in coupled transcription/translation reactions to obtain the proteins of interest.

Recent developments in DNA/RNA chemical synthesis have allowed us to attach some functional groups covalently to nucleic acids, thus permitting the introduction of a functionality or properties not normally present in the native biomolecule The use of non-nucleosidic linkers is probably the most popular approach for the 5 -terminal modification of chemically synthesized nucleic acid oligonucleotides and a number of such linkers are commercially available. The linker shown in Fig. 2 is designed as a phosphoramidate derivative so that it can be incorporated into the 5 -terminus of the sequence as the last... 

Synthetic oligonucleotides are very important tools in the study and manipulation of DNA, including such techniques as site-directed mutagenesis and DNA amplification by the polymerase chain reaction. The techniques for chemical synthesis of oligonucleotides are highly developed. Very efficient automated methodologies based on solid phase synthesis are used extensively in fields that depend on the availability of defined DNA sequences.52... 

Chemical synthesis, an approach limited by complex synthetic sequences using protection of hydroxyl groups to achieve regio- and stereo-selectivity... 

An alternative approach to the production of subunit vaccines entails their direct chemical synthesis. Peptides identical in sequence to short stretches of pathogen-derived polypeptide antigens can be easily and economically synthesized. The feasibility of this approach was first verified in the 1960s, when a hexapeptide purified from the enzymatic digest of tobacco mosaic virus was found to confer limited immunological protection against subsequent administration of the intact virus. (The hexapeptide hapten was initially coupled to bovine serum albumin, used as a carrier to ensure an immunological response.)... 

Solid-supported technologies are already well established methods in medicinal chemistry and automated synthesis. Over the last couple of years new trends have evolved in this field which are of utmost importance as they have the potential to revolutionize the way chemical synthesis especially for library production is performed. Microchip-based synthesis technologies and multistep sequences with solid-supported catalysts or reagents in flow-through systems are only two spectacular examples. A new approach is the use of solid-supported systems for the scale-up of chemical reactions thereby enabling the rapid and smooth transition from discovery to development units. 

The preparation of a combinatorial library requires the simultaneous manipulation and isolation of many different compounds. A uniform sequence of operations is required to efficiently prepare and isolate each member of the library. In contrast the traditional synthesis of compounds utilizes conditions tailored specifically to the compound desired. A key challenge for library preparation is the development of a robust synthesis sequence that cleanly incorporates chemical building blocks containing a diverse range of chemical functionality in high yields. Equally important are the development of uniform and efficient methods to isolate intermediates and products from solvents, reagents, and byproducts. 

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