Molecular Medicine

This page contains abridged crux of lecture topics covered during the course.

Molecular Biology Techniques 

In order to understand pathogens at a molecular level and conduct research, specific molecular biological techniques are utilized to study the interactions of nucleic acids and enzymes. This allows for the detection of disease progression (prognosis), abnormal states (diagnosis), and normal states (diagnosis) in humans. Nucleic acids are essential in understanding molecular pathology; this is the genetic material for all living organisms that code for certain genetic information.

DNA and RNA and the basic building blocks of genetic material. These nucleotides are made of nitrogenous bases, a phosphate group and a 5 carbon sugar (either ribose or deoxyribose) interact through hydrogen bonds. Base pairings are formed between two types of bases, purine, and pyrimidine. While purines are fused five- and six-membered rings (adenine & guanine), pyrimidines are also six-membered (cytosine, thymine & uracil). A purine would naturally pair with a pyrimidine. Thus the bonds holding the base pairings are called hydrogen bonds. 

Restriction Enzymes - Specific endonucleases detect sequences of DNA phosphodiester bonds and cleave them; this is called a restriction enzyme. These recognition sequences typically vary from 4 or 6 bases to 5 or 8. These aid in isolating genes and diagnosing DNA sequences in modern medicine, making restriction enzymes indispensable in the medical field. 


Nucleic acid Hybridization - Identifying particular genes or DNA sequences requires nucleic acid hybridization with probes. Hybridization between nucleic acids form a duplex consisting of two complementary strands, the term “annealing” refers to this process. Probes are an additional nucleic acid which aids in hybridization through labeled markers in identification and quantitation. Specific labels include FISH (fluorescent in situ hybridization), Radioactive, and Biotinylated labels. 

Polymerase chain reaction (PCR) - PCR is the synthesis and amplification of DNA sequences, and this process allows for the numbers of specific DNA sequences to be amplified in little time. Applications of PCR include HLA typing or the detection of pathogens. Methods and specific enzymes are used in particular due to the large complexity of genomic expression. Each individual has minor genetic differences in base sequences, forming variations of genomes worldwide. 

Restriction Fragment Length Polymorphism - RFLP (restriction fragment length polymorphism) is an allele identified based on either the presence or absence of a restriction enzyme site. These polymorphisms affect how proteins interact and contribute to phenotypic differences among individuals. Therefore polymorphisms such as RFLPs or SNPs (single nucleotide polymorphism) acting as biological markers contribute to the location of genetic mutations in the body, playing an essential role in the medical field.

Hallmarks of Cancer

Cancer is the progression of which cells divide uncontrollably in an abnormal environment. This allows for abnormal cells to spread throughout the body using blood and lymph systems. Cancer can manifest in various ways. Therefore classifications for the types of cancers are necessary to understand how cancer grows. Tumors can be broadly classified into solid tumors and liquid tumors. Some examples of each include carcinoma, sarcoma, central nervous system cancers and leukemia, lymphoma myeloma, etc.

Hanahan, Douglas. “Hallmarks of Cancer: The Next Generation.” Cell, 4 Mar. 2011, 

www.cell.com/fulltext/S0092-8674(11)00127-9.

Cancer cells' hallmarks are characteristics that equip these cells to grow and divide uncontrollably. metastasis, including evasion of 

Although these hallmarks are distinctive and individually characterized for different categories of cancer, such characteristics provide basics for research and development for medicine for various types of cancer. Considering the factors that have to be accounted for in cancer drug development, it is significant to continuously learn and be updated with scientific advances in addition to having medical training. This can help consider all symptoms of a specific individual when prescribing a patient. 

Clinical Trials


Clinical Trials are a series of experiments planned to evaluate potential treatment and therapy developments. These are studied with as many controlled conditions as possible in order to prevent confounding variables within the potential treatments. Clinical Trials determine the most practical and definitive benefits in treatments, considering other variables such as side effects and other complications. In initiating Clinical Trials, there must be definitive answers to why, who, what, which, where, when and how in developing medicines for extremely sick patients.  These elements assist in identifying the most effective potential treatment to be marketed.

In Phase, I trials, primary and secondary objective is to determine the drug's safety in humans. This is where the drug is determined for toxicities and range of doses, as well as identifying the drug's Pharmacokinetics (PK) and Pharmacodynamics (PD). 

In Phase II trials, therapeutic activity is screened and the drug's toxicity evaluation is further analyzed. This is to evaluate if there is any benefit to the patients from the drug. Once the drug's activity is screened in Phase II trials; Phase III trials are initiated. 

Phase III trials contribute to the large multi country studies , where new/researched drug treatment is compared with other previous effective therapies. Phase III studies are to confirm that results from Phase II studies are indeed accurate and there is benefit in a large number of patients across multiple countries. 

Approval of drugs - Several agencies evaluate all the data collected by these clinical trials and determine if the drug will add true value to patient care.  FDA, EMA are some of the examples of the agencies that approve drugs in different continents. 

In some cases these drug approving agencies might request additional data from Phase IV trials, which further expand on controlled conditions and safety within the treatment for widespread marketing. 

Drug Discovery & Development


Drug discovery and development is discovering substances that can have medicinal value for diseases. Once such substance is identified, it is actively developed via specific steps and protocols. The entire process is very long and thorough to ensure that great attention is paid to develop effective drug and that it can bring potential benefit treatment for the population. The very rationale of the drug should be determined first. Therefore the lead compound and objective disease treated must be identified. 


Target identification - The target of the drug is identified next, specifically targeting a specific macromolecule or what the drug will be interacting with. 


Target validation - This is further analyzed through bioassays including, in vitro testing, in vivo testing and ex vivo testing for screening and efficacy, thus determining what the body does to the drug (pharmacokinetics) and what the drug does to the body (pharmacodynamics). 


In finding the lead compound or determining the lead compound structure, screening natural products or stored compounds can be cataloged and identified as lead compounds. In addition, picking up leads from the same previous combinations to enhance it has been done before, the possibilities in identifying a lead are not limited to brand new products. Once a lead candidate has been found, an essential step is to understand the pharmacophore, in which are the structural features of the molecules in the compound that are responsible for biological activity. 


Improving pharmacokinetic properties - This is the next step to developing a drug, which enhances the absorption, distribution, metabolism and excretion of a drug (ADME). When the drug is initially absorbed in the body, it rejects it as it is not a natural substance. Although these substances are referred to as "xenobiotics", the body makes it a point to eliminate them through excretion. Therefore the body attempts to transform the xenobiotics into polar substances as the kidneys allow polar substances to be excreted through urine.  After the drug is developed, it must undergo a series of clinical trials to be approved for mass production and manufacturing, where patients and side effects are monitored for a higher quality of life.


Cell and Gene Therapy


Gene therapy is a treatment in which a therapeutic gene is placed inside a patient's cells to treat a particular disease, whereas Cell therapy is a treatment in which specific cells are placed inside a patient to treat a particular disease. Though these therapies often remain disparate, Cell/Gene therapy has recently been used to treat HIV, an immunological disease. Cell/Gene therapy approaches the treatment of inserting genes into a patient's own cells to control or kill a condition. Different routes for gene therapy are available such as in vivo and ex vivo gene therapy. Ex vivo gene therapy involves genes of a specific patient being genetically engineered outside of the body to produce therapeutic effects to transplant back into the same patient. In vivo gene therapy consists of the usage of viruses or transplantation of newly modified genes of which were not previously associated with the patient's body. 


In treating HIV through Cell/Gene therapy, Hematopoietic Stem Cells (HSCs) are transferred out of the patient's body to modify into a particular CCR5 gene deletion to enhance the elimination of the virus. This is further expanded and corrected before transplanting back inside the body, in which a new generation of genetically modified HIV-protected blood will continue inside the patient. Other Cell/Gene therapy approaches include modifying and replicating functional killer cells that can suppress the HIV infection from spreading across cells by elimination, or T-cells are taken out of the patient's body and presented with HIV antigens to properly identify the HIV inside the immune system. 


In conclusion, this Cell-Gene therapy is a growing medical field that offers promise in cures and treatments for potential diseases such as HIV. Although current approaches are complex and complicated, the fast-growing technology in the modern world will allow for more straightforward and cheaper therapies.

Cell Therapy 


Cell therapy is a treatment in which live cells are transplanted inside a patient to receive therapeutic or medicinal effects; therapies that use cell therapy, such as stem cell therapy and chimeric antigen receptor (CART) cell therapy, have been used in recent times to treat certain diseases. 

In stem cell therapy, various stem cells can derive from different origins. These stem cells have different usages for each type; somatic autologous stem cells are known for differentiation into tissue-related cells. Their differentiation characterizes adult mesenchymal stem cells (MSCs) into skeletal tissue cells whereas induced pluripotent stem cells (iPSCs) are cells deriving from the blood, heart or skin that are reprogrammed into an embryonic-like pluripotent state which allows for the differentiation of any kind of animal human cell needed. Cord blood allogeneic hematopoietic progenitor stem cells (HSCs) are most commonly transplanted and used across the medical field for its flexibility in therapeutic effects for diseases and handling side effects such as graft vs host disease. 

Chimeric Antigen Receptor T-cells (CAR T) are genetically engineered T-cells modified to express a CAR complex. This refers to the modified immunoreceptor engineered to recognize a particular target from a monoclonal antibody. CAR T cells can target diseases that the immune system cannot recognize, such as leukemia or HIV. Likewise, to stem cells, CAR T cells have a variety of cells that target different surface proteins for treating different diseases. 


Cancer Therapy


Cancer is a wide range of different variations and derivations, as well as the fact that the basis of cancer symptoms are its characteristics as hallmarks. Therefore, it is crucial to realize the necessity of multiple cancer treatments. Treatments such as chemotherapy, radiation therapy, targeted therapy, and immunotherapy are current modern treatments used in cancer patients depending on their symptoms. 


Chemotherapy: Chemotherapy involves drugs given to a cancer patient to eliminate cancer cells inside the body. This allows the cancer cells to either be eradicated or controlled at a minimum to prevent metastasis. In chemotherapy, commonly used drugs are-

These drugs often interfere with the cell division processes, either disturbing the microtubules and spindle fibers during mitosis (cell-cycle specific agents) or damaging the DNA (cell-cycle nonspecific agents). The lack of specific activity of these drugs on cancer cells causes the side effects of chemotherapy such as hair loss or anemia. These drugs eradicate non-cancerous cells and cancer cells, resulting in a lack of differentiated cells in certain body parts. 


Targeted therapy:  These drugs are given to cancer patients that precisely recognize and attack specific cancerous cells. Targeted therapies are often combined with other therapies such as radiation therapy or chemotherapy. Deriving agents that come from targeted therapy are either small molecules or monoclonal antibodies. 


Radiation therapy: requires the usage of high-energy electromagnetic radiation to eliminate or shrink cancer cells or tumors through direct damage of the DNA, rendering cell division inconceivable. This radiation can either be delivered, externally, internally or systemically. 


Immunotherapy: Although current methods effectively control cancer cells, certain drawbacks such as tumor resistance or side effects that cancer patients acquire from these treatments pull these therapies back. Treatments such as CAR T therapy (chimeric antigen receptor) or autologous cellular immunotherapy is being used to aid in eliminating cancer cells through less straining means for the patient. This new modern technology in genetic engineering allows newer generations to continue to thrive further, creating a safer and healthier environment for the future.