A new paradigm has emerged for drug development and patient care. It is a fusion of traditional and modern medicine, or systems and reductionist thinking. In the 21^st century, mathematics, the foundation of modern science, is being used to analyze biological networks to help discover and improve new drugs. In both traditional and modern medicines, it is important to know about the individual components of cells: DNA, RNA, proteins, lipids and carbohydrates, so these are described. There is a division of labor in cells. DNA and RNA are used to store and process genetic information, while proteins, lipids and carbohydrates primarily perform metabolic and structural roles. DNA can code for proteins and different types of RNAs. The former dogmas that DNA codes for mRNA, which codes for proteins and one gene codes for one protein, are only partly right. This does occur, but also pieces of DNA from different chromosomes can be mixed and matched to make millions of different proteins. Genes can be made of DNA or RNA. Some proteins also help control the expression of genes and work with self-assembled ribosomal RNAs to make themselves and other proteins in ribosomes. There are also mobile genetic elements, also known as jumping genes and transposons. LINE 1 retrotransposons make up about 20% of the human genome and can move around in it. Many retrotransposons are active in the hippocampus and caudate nucleus in the human brain and may account for much of the differences that are seen in so-called identical twins (actually, monozygotic twins). Moreover, about 76% of human DNA is transcribed into different types of RNA. There are also the crucial parts of the human genome that code for the microRNAs or miRNAs, which help control which mRNAs are translated into proteins and which are not. Genes can also be silenced by small interfering RNA, or siRNA. Another class of RNA is the long intergenic non-coding RNA, or linc-RNA. They are involved in diverse biological processes, including regulating the cell cycle and helping to maintain the pluripotency of stem cells. Genetic engineering can also be used to make genetically modified (GM) bacteria, which can produce medicines, such as insulin for diabetics. Insulin is a polypeptide. There are also epigenetic mechanisms that can affect the ability of a gene to be transcribed or an mRNA to be translated into a protein. This is because we are coupled to the environment. We change our structure in response to environmental conditions, and we change the internal and external environments in response to our needs. Proteins that bind to RNA can control how DNA is transcribed. There are also sugars and carbohydrates that can provide fuel and energy through glycolysis and the citric acid cycle, as well as bind to proteins, to affect their properties. Lipids make up the cell membrane and intracellular membranes of internal organelles. They can interact with proteins and carbohydrates. Specific lipids can bind to important proteins, affecting their function. Polyunsaturated omega-3 fats are especially healthy and can help prevent inflammation and help resolve inflammation quickly when it does occur.

Biotechnology is the use of technology to study biology and develop new drugs. For example, genetic engineering tools were used to solve the human genome and may lead to the production of new types of bacteria, algae and other life forms that will make many of the products that are now made from fossil fuels. Pieces of DNA can be cut from chromosomes using restriction endonucleases and other forms of genome editing. Clustered, regularly interspaced, short palindromic repeats, abbreviated as CRISPRs are especially useful. The pieces of DNA are inserted into vectors made from viruses or artificial chromosomes to make recombinant DNA. They are inserted into bacteria where enough copies of them are made to enable DNA sequencing. Biotechnologies can be used to determine the genome and proteome of cells. Also, instead of making prescription drugs from small molecules by chemical synthesis or purification from natural sources, some of them can be made using biotechnologies. That is, genetic engineering can be used to insert (recombine) the gene that codes for them or the enzymes needed to biosynthesize them into vectors. The vectors can be inserted into bacteria, yeasts, plants and animals. Also, larger therapeutic molecules can be made. This can include antibodies, DNA, RNA and even whole cells. Antibiotics, vitamins, vaccines and natural products can also be made. Not only genes, but also smaller pieces of single-stranded DNA or RNA oligonucleotides (5-40 kDa) called aptamers can be used therapeutically [1]. Also, catalytic ribozymes, small interfering RNA (siRNA), RNA aptamers, short hairpin RNA (shRNA), bifunctional shRNA and microRNA can be used to knock down specific proteins [2]. Finally, whole cells can be used therapeutically. This includes immune cells, glial progenitor cells, embryonic stem cells, vaccines and even fecal transplants.

Drugs are sometimes developed in distinct phases. Usually, the drug discovery and development process can be divided into these stages: select a disease, identify a target, find a lead compound, quantify drug-target interactions, determine solubility, pharmacokinetics and toxicity, improve the lead compound, find the best way to deliver the drug to the patient, manufacture the drug, apply to the FDA to do investigational studies, do the clinical studies, apply to the FDA for drug approval, and do post-registration studies [1]. The solubility, pharmacokinetics and toxicity are determined in GLP studies. Similar compounds are tested in the lab and by computer modeling, so structure-activity relationships (SARs) can be developed. Eventually, a new chemical entity (NCE) or investigational new drug (IND) is selected for further evaluation. The optimum method for drug delivery is selected. A manufacturing process is developed and documented according to cGMP. Potential targets include membrane bound receptors (such as GPCRs, tyrosine kinases and intracellular nuclear receptors). Agonists bind to receptors and mimic the action of the endogenous ligand. Antagonists bind to receptors and block the binding and subsequent action of the endogenous ligand. Enzymes, DNA, protein transporters, ion channels and pumps are other potential targets.They are part of the cellular network. Most nodes in cellular networks can be thought of as problem solvers. For example, the enzymes in glycolysis catalyze reactions that are needed to produce energy. Hubs, though, act as problem distributors. They distribute signals to many other nodes, in response to changes in the intra- and extracellular environments. Both problem solvers and distributors can be predictable. Another type of node is less predictable and is called a creative element. These nodes are quite dynamic and monitor almost the entire network by continuously changing the structures of the proteins to which they are linked. Creative elements may have few links at a given time, but can increase their connectivities when needed.

Pharmacokinetics is the science of determining how much of the drug reaches the target organs and how much is eliminated at different times after giving different doses, sometimes in various dosage forms. Toxicokinetics is similar to pharmacokinetics, except one is concerned with toxins, as opposed to medicinal drugs. However, when the dose of a medicinal drug becomes too high, it becomes toxic. So, toxicokinetics is much like pharmacokinetics, but at a higher dose. Important parameters include the maximum drug concentration, Cmax, the time it takes to reach maximum concentration, T_max, the area under the curve, AUC, bioavailability, clearance, volume of distribution and the half-life [1] for clearance, t_1/2. Physiological based pharmacokinetic models (PBPK) match the individual compounds’ properties to their physiological properties. This is a rational approach for predicting their pharmaceutical properties [1] in vivo. Drug metabolism occurs mostly in the liver and intestine. Phase I metabolism adds functional groups (-OH, -SH, -NH₂, -COOH), while phase II involves biotransformation. Phase II enzymes add larger molecules and groups. Drugs can have multiple effects on the proteome, transcriptome, epigenome, metabolome and interactome of cells, tissues and organisms.

The first rule of toxicology is that the dose is the poison. That is, every substance is toxic if given at a high enough dose. Toxicity testing in animals (usually rodents) is required for investigational new drugs. The EPA does toxicity tests on environmental chemicals through the National Institute of Environmental Health (NIEHS) and the Environmental Toxicology Program (ETP). They give very large doses of test chemicals to rodents to see if they might be harmful to the small portion of humans who are highly susceptible to the test chemical. GLP was formulated by the US Food and Drug Administration (FDA) to regulate non-clinical studies on the safety and possible toxicity of a new compound. The European Medicines Agency (EMA) has its own GLP regulations that overlap with the FDA GLP. Every GLP study must have a study director, who writes a study protocol and is responsible for the design, conduct and reporting of the study. Many GLP studies also have principal investigators (PIs). In contract labs that work for the NIEHS, there is a single PI who has overall responsibility for the GLP studies. The PI must approve of all study protocols and any amendments.

To improve the lead compound, chemists can do rational drug design. They can systematically alter the structure of the lead compound to provide different compounds that are more effective and have fewer side effects. The structures of compounds drawn in silico can be docked to the target proteins and interaction energies calculated. Databases of biochemical and medicinal interactions can be evaluated using network theory to find new targets for therapy. Computer programs can be used to calculate molecular and quantum mechanical descriptors, which can be correlated to the measured properties in a quantitative structure-activity relationship, or QSAR. Other tools of rational drug design are to model molecular structures and their binding to potential targets, do combinatorial synthesis and high throughput screening for any of a number of biological effects. One can also look for the genetic cause of a disease and a way to deliver the correct gene into the patient in gene therapy.

Medicinal chemists try to find ways to get drugs to the target cell and organ, and not to the rest of the body, and to activate the drug only at the target organ, to make it effective. This can be done with liposomes, synthetic polymers, dendrimers and nanotechnology. Liposomes prepared from polyethylene glycol (PEG) are used to deliver the anticancer agent doxorubicin. Another way to deliver drugs to their specific target is through antibody-drug conjugates and fusion proteins, in which one part (such as the antibody) binds specifically to the target and the other part is released and has the desired therapeutic effect. An example of this is the drug called trastuzumab emtansine, also known as T-DM1. There are also recombinant immunotoxins, in which a fusion protein is made that contains a bacterial toxin and a fragment which targets the specific cancer cells being treated. An example is anti-Tac(Fv)-PE38 or LMB-2, which contains a toxin fragment of Pseudomonas endotoxin and a monoclonal antibody against the cell surface protein, CD25, in cancer cells. Another example that is in development is targeted delivery of small inhibitory RNAs (siRNAs).

If a drug formulation is proved to be safe and effective with animals, more must be made to start testing in humans. Before this can happen, “an Investigational New Drug Application (IND)” [1, 2] must be filed with the FDA [1, 2]. FDA has a set of quality controls for drug manufacturing, called current Good Manufacturing Practice, or cGMP. The FDA audits manufacturing organization and it can issue FDA form 483 and a warning letter. Methods used to analyze new chemical entities include UV-Vis and fluorescence spectrophotometry, HPLC and UPLC, ion chromatography, gas chromatography (GC), mass spectrometry (MS), GC-MS [3], LC-MS, IR and NMR. UV-Vis spectrophotometry measures the absorbance of UV and/or visible light. The wavelengths absorbed depend on the type of compound being analyzed and the amount of absorbance “depends on the amount present in the sample” [3]. Fluorescence spectrophotometry measures the emission of light that occurs at a longer wavelength than the light that is used for excitation. Ion chromatography separates and detects ions. Gas chromatography separates molecules in the gas phase and detects them using any of a number of detectors, including MS. Infrared (IR) spectroscopy measures the absorbance of IR light, which provides information about the compound being analyzed. NMR measures the absorbance of radio frequency electromagnetic radiation when organic compounds are placed in a strong magnetic field [3]. It can tell the analyst how many hydrogens and carbons there are in the sample, along with the hydrogens and carbons to which they are bound.

New drugs are investigated in the following steps: pre-clinical, phase I, phase IIa, phase IIb, phase IIIa, phase IIIb, launch new FDA-approved drug and phase IV, post market surveillance [1]. The pre-clinical phase is used to prove the scientific principal behind the drug, perform 28 day toxicity studies in two species, identify a suitable formulation, prepare sufficient material, perform an Institutional Review Board review, and prepare protocols and documents for Phase I. Phase I measures the absorption, distribution, metabolism and excretion (ADME) [1] safety and tolerability in healthy human subjects, except in emergencies, such as treating terminally ill cancer patients for whom all standard therapies have been tried already. Phase IIa tests the efficacy of the IND and its ADME in patients and IIb establishes the dosage and regimen for Phase III. Phase III is the large scale clinical trial that will determine the efficacy and look for side effects. After getting FDA approval and launching the new drug, the market must be monitored so that all side effects and complaints are saved and studied. Also, additional applications for the drug might emerge as it is used on patients with more than one condition that needs to be treated.

There are many important drugs that inhibit enzymes. They include drugs to prevent heart attacks, pain relievers, antibiotics to cure bacterial infections, chemotherapeutic drugs to help cure cancer, anti-malarial drugs, sleeping pills, medicines for high blood pressure, and drugs to treat diabetes, asthma, HIV, seasonal flu, fungus infections, parasitic worm infections and osteoporosis. Enzymes that are inhibited by FDAapproved drugs include acetylcholine esterase, AChE; cyclooxygenase; enzymes that catalyze a key reaction in the synthesis of bacterial cell walls; the protein-RNA complex of the 30S subunit of the bacterial ribosome; bacterial DNA-gyrase; topoisomerase; bacterial tetrahydrofolate reductase; a reductase that catalyzes the synthesis of mycolic acids in Mycobacterium tuberculosis; angiotensin-converting enzyme, or ACE; renin; type 5 phosphodiesterase (PDE-5); farnesyl pyrophosphate synthase; inosine-5’-monophosphate dehydrogenase (IMPDH); calcineurin; HIV reverse transcriptase; fungal enzymes; pyruvate-ferridoxin oxidoreductase; aromatase; topoisomerase; BCR-ABL tyrosine kinase; the proteasome,; histone deacetylase,; thymidylate synthase; viral neuraminidase, viral thymidine kinase; L-amino acid decarboxylase; xanthine oxidase; and dipeptidyl peptidase- 4 (DPP-4). Drugs are being developed that bind to allosteric sites on enzymes, partially inhibiting them and causing fewer side effects than drugs already developed that target active sites.

There are many important drugs that bind receptors. Morphine, codeine and heroin and fentanyl bind to opioid receptors. Barbituates, zolpidem and diazepam bind to GABAA receptors. Varenicline binds to nicotinic acetylcholine receptors; Tiotropium bromide binds to the M3 muscarinic acetylcholine receptor. Tamsulin binds α_1aadrenergic receptors in the prostate; bronchodilators bind to β₂-adrenergic receptors. Ramelteon binds to the melatonin receptor and lets the patient sleep. Memantine binds to the NMDA subset of glutamate receptors. Montelukast sodium is a synthetic antagonist of a cysteinyl leukotriene receptor. Loratadine blocks the binding of histamine to its receptor. Prostaglandin analogs, such as latanoprost decrease intraocular pressure by binding to prostaglandin receptors. Ranitidine binds to the histamine H2 receptor. Glipizide binds to K⁺ ion channels in the β cells of the pancreas. Pioglitazone is an agonist of the peroxisome proliferator-activated receptor-γ, or PPARγ. Atenolol binds competitively to the β-adrenergic receptor and blocks the binding of the natural ligands, adrenaline and noradrenaline. Calcium ion channel blockers like Amlodipine decrease contractions of the heart and dilate the arteries, lowering blood pressure. Clopidogrel bisulfate prevents the formation of blood clots by inhibiting the binding of ADP to its platelet receptor. Estrogens and progestins bind to estrogen receptors and progesterone binds to its receptor. Oxytocin binds to G-protein coupled receptors (GPCRs). Calcitriol binds to the Vitmin D receptor. Raloxifene is a selective estrogen receptor modulator. FY720 binds to the sphingosine-1-phosphate receptor. Vaccine adjuvants bind to toll-like receptors. UK-427857 (Maraviroc®) binds to the CCR5 receptor, preventing the binding of HIV.

Another important class of proteins that make good targets for drugs is the class that contains transporters, carriers and ion pumps. There are several drugs that affect ion pumps, carriers and transporters. Ezetimibe (Zetia®) inhibits the absorption of dietary cholesterol in the small intestines. Stomach acid is produced by one type of H⁺/K⁺ ATPase. The drugs called Omeprazole (Prilosec®) and Prevacid inactivate it. Atovaquone and Proguanil act by inhibiting electron transport. Ion pumps are also important in multidrug resistant (MDR) bacteria and cancer cells. Ivermectin (Stromectol®) is a broad spectrum antiparasitic agent that acts by opening glutamategated chloride channels in invertebrates. MDR in cancer involves simultaneous resistance to several different, unrelated anticancer drugs. An efflux protein, P glycoprotein, or PgP, pumps out anticancer drugs. There are several other drugs, called MDR converters that inhibit the action of PgP.

Microtubules and proteins that bind to them are also possible targets for therapy. They participate in many cellular processes, including transport and cell division. There are two major classes of microtubule drugs, microtubule destabilizers (or inhibitors) and microtubule stabilizing agents. However, tumors develop resistances to microtubule inhibitors. This has many causes, but some of the most important are “efflux pumps such as the P-glycoprotein or ABCG2 and MRP1. Thus, the identification of compounds that are active in multidrug-resistant (MDR) cells is urgently needed” [1]. There are two classes of microtubule drugs, microtubule inhibitors (vincristine and vinblastine, which are alkaloids from the Madagascar periwinkle, also known as the Catharanthus roseus, and once known as Vinca rosa), approved by the FDA in 1963 and 1965, and stabilizers Taxol (Paclitaxel) and Taxotere (Docatexel) approved in 1992, and 1996, respectively. Also, there are two semi-synthetic derivatives of vincristine, called vindesine and vinorelbine. Another class of microtubule-acting anticancer drugs contains the epothilones. “Epothilones A and B are naturally occurring 16-membered macrolides, which are produced by the myxobacterium Myxococcus xanthus or Sorangium cellulosum” [1]. Another natural product that acts on tubulin is called eribulin. It was isolated from the Pacific sponge and it inhibits the polymerization of tubulin. The root bark of the Combretum caffrum tree is the source of combretastatin, which is another natural inhibitor of tubulin polymerization [1]. Another drug that binds to microtubules is called Maytansine. It disrupts microtubule assembly.

Some drugs target or use DNA or RNA. One of the most important is called either adriamycin or doxorubicin. Another, mitomycin is activated in liver cells and adds an alkyl group to bases, causing DNA to cross-link, which kills the cancer cells. Another alkylating agent is Ifosfamide, which is used to treat testicular cancer, breast cancer, lymphoma, testicular cancer, cervical cancer, bone cancer, soft tissue sarcoma, osteogenic sarcoma, and ovarian cancer [1]. Carboplatin (Paraplatin®) is a chemotherapeutic agent for treating cancer. Bleomycin (Blenoxane®) is a member of a family of glycopeptide antibiotics produced by Streptomyces verticillus. It damages deoxyribose in DNA, causing the strand to break. It is used to treat testicular cancer, along with head and neck cancer. There are also antimetabolites and nucleosides that are FDA-approved anti-cancer agents. They include 5-azacytidine, 5-fluorouracil, 6- mercaptopurine, allopurinol, calcium leucovorin, capecitabine, cladribine, clofarabine, cytarabine, decitabine, “floxuridine, fludarabine, gemcitabine, hydroxyurea, methotrexate, nelarabine, pemetrexed, pentostatin and thioguanine” [1]. Vitravene is an antisense drug that binds to mRNA that is produced by a gene coded by the cytomegalovirus (CMV), which causes CMV retinitis. DNA can also be used as a drug in gene therapy.