Drug Discovery NDD (New Drug Development).pptx

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1. Foundation Course Drug Discovery & New Drug Development (NDD) 1

2. Drug discovery process 2

3. DRUG DISCOVERY TIMELINES 3

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11. Step 1. Pre-discovery Understand the disease  The pre-discovery stage begins with “basic research, fundamental knowledge, and understanding of the mechanisms of pathology.” Before any potential new medicine can be discovered, scientists work to understand the disease to be treated as well as possible, and to unravel the underlying cause of the condition. They try to understand how the genes are altered, how that affects the proteins they encode and how those proteins interact with each other in living cells, how those affected cells change the specific tissue they are in and finally how the disease affects the entire patient. This knowledge is the basis for treating the problem. Researchers from government, academia and industry all contribute to this knowledge base. However , even with new tools and insights, this research takes many years of work and, too often, leads to frustrating dead ends. And even if the research is successful, it will take many more years of work to turn this basic understanding of what causes a disease into a new treatment. An important part of early pharmaceutical research is determining if there is an unmet need in the industry. This refers to diseases where there is currently no appropriate medicine; or there is medicine available but the side effects are too severe.  If the researcher finds that there is an unmet need, they will continue with their research and development to develop a new medicine for their targeted disease. 11

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14. Step 2: Target identification/Target discovery Target identification is the ultimate goal of the pre-discovery phase of pharmaceutical research. The pre-discovery stage allows researchers the time to understand the disease and choose a valid target molecule. This understanding allows for the potential of discovering and developing more advanced medicines. Once the researcher has identified the unmet need, they must understand the disease at a molecular level.  They will study  “how genes have changed, how these changes affect the proteins encoded by the genes, how those proteins interact with each other in living cells, how the affected cells change the specific tissue they are in, and how all these processes combine to affect the patient.” Once this is completed, they will choose the biological target for a prospective medicine.  The biological target is a “ biomolecule , which is involved in that particular disease and can be modulated by a drug.” The drug target is a biomolecule(s), normally a protein that could exist in isolated or complex modality. The biomolecules have special sites that match other. The bio molecular structure might change when the biomolecule binds to small molecules and the changes in structure normally are reversible. Drug target interaction  is a prominent research area in the field of  drug  discovery. It refers to the recognition of  interactions  between chemical compounds and the protein  targets  in the human body. 14

15. The second step in drug development is to discover or identify a target or treating or preventing a disease. Targets are usually proteins or genes or hormones which are associated with a disease or causing a disease. The challenge is to identify which proteins are relevant and or importantly confirm their needs role in a disease. . Targets include :A   drug target  is a molecule in the body, usually a protein, that is intrinsically associated with a particular disease process and that could be addressed by a  drug  to produce a desired therapeutic effect.          Receptors          Enzymes          Hormones and factors          Nuclear receptors          DNA          Ion channels Target identificationcan be achieved by numerous methods including; affinity chromatography, expression-cloning, protein microarray, 'reverse transfected ' cell microarray, and biochemical suppression. 15

16. Nearly all diseases have a genetic component. Some diseases are caused by mutations that are inherited from the parents and are present in an individual at birth, like sickle cell disease. Disease gene identification allows accurate diagnostic testing in patients and prenatal, presymptomatic , and carrier testing in unaffected family members; The analysis of candidate genes is a key step in strategies for disease gene identification and includes: (1) identifying candidate genes that might have a role in the etiology of the disorder; (2) identifying variants in or near those genes that might cause a change in the protein or its expression; or (3) assessing the sequence. Also due to their central role in biological function, protein interactions also control the mechanisms leading to healthy and diseased states in organisms. Diseases are often caused by mutations affecting the binding interface or leading to biochemically dysfunctional allosteric changes in proteins. Because form determines function, any slight change to a protein's shape may cause the protein to become dysfunctional. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington's disease or sickle cell anemia. .. They also assist with the formation of new molecules by reading the genetic information stored in DNA. Messenger proteins, such as some types of hormones, transmit signals to coordinate biological processes between different cells, tissues, and organs. These proteins provide structure and support for cells 16

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19. Examples The coronavirus disease (COVID-19) pandemic is sweeping the globe. Even with a number of effective vaccines being approved and available to the public, new cases and escalating mortality are climbing every day. ACE2 (angiotensin-converting enzyme 2) is the primary receptor for the COVID-19 causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and its complexation with spike proteins plays a crucial role in viral entry into host cells and the subsequent infection. ACE2 represents a promising target to attenuate or prevent COVID-19 associated cellular injury. ACE2 protein expression is present in heart, kidney, testis, lung (type I and type II alveolar epithelial cells), nasal, and oral mucosa and nasopharynx (basal layer of the non-keratinizing squamous epithelium), smooth muscle cells and endothelium of vessels from stomach, small intestine and colon, in smooth muscle . Blocking this binding event or reducing the accessibility of the virus to the ACE2 receptor, represents an alternative strategy to prevent COVID-19. In addition, the biological significance of ACE2 in modulating the innate immune system and tissue repair cascades and anchors its therapeutic potential for treating the infected patients. In this viewpoint article, we review the current efforts of exploiting ACE2 as a therapeutic target to address this dire medical need. We also provide a holistic view of the pros and cons of each treatment strategy. Hence, laboratories worldwide are developing an effective vaccine against this disease, which will be essential to reduce morbidity and mortality. Currently, there more than 64 vaccine candidates, most of them aiming to induce neutralizing antibodies against the spike protein (S). These antibodies will prevent uptake through the human ACE-2 receptor, thereby limiting viral entrance. 19

20. The breast cancer cells have receptors on the outside of their walls that can catch specific hormones that circulate through your body. Knowing your breast cancer is sensitive to hormones gives your doctor a better idea of how best to treat the cancer or prevent cancer from recurring. Hormone status of breast cancers includes: Estrogen receptor (ER) positive.  The cells of this type of breast cancer have receptors that allow them to use the hormone estrogen to grow. Treatment with anti-estrogen hormone (endocrine) therapy can block the growth of the cancer cells. Progesterone receptor (PR) positive.  This type of breast cancer is sensitive to progesterone, and the cells have receptors that allow them to use this hormone to grow. Treatment with endocrine therapy blocks the growth of the cancer cells. Hormone receptor (HR) negative.  This type of cancer doesn't have hormone receptors, so it won't be affected by endocrine treatments aimed at blocking hormones in the body. Tamoxifen . This drug blocks estrogen receptors on breast cancer cells. It stops estrogen from connecting to the cancer cells and telling them to grow and divide. While tamoxifen acts like an anti-estrogen in breast cells, it acts like an estrogen in other tissues, like the uterus and the bones. 20

21. Step 3. Validate Target Target validation is  the process by which the predicted molecular target  – for example protein or nucleic acid – of a small molecule is verified. The physiological, cellular, and/or genetic basis of a disease is studied to identify potential therapeutic targets. Target validation  is the next step in  discovering  a new  drug  and can typically take 2-6 months. The process involves the application of a range of techniques that aim to demonstrate that  drug  effects on the  target  can provide a therapeutic benefit with an acceptable safety window. Target Validation shows that a molecular target is directly involved in a disease process, and that modulation of the target is likely to have a therapeutic effect. After choosing a potential target scientist must show that it is actually involved in the disease and can be acted upon by drug. Target validation is crucial to help scientist avoid research paths that look promising but ultimately lead to dead ends. Researcher demonstrate that a particular target is relevant to the disease being studied through complicated experiments in both living cell and in animal model. Target validation is the process of demonstrating the functional role of the identified target in the disease phenotype. Whilst the validation of a drug’s efficacy and toxicity in numerous disease-relevant cell models and animal models is extremely valuable – the ultimate test is whether the drug works in a clinical setting. 21

22. Validate Target (continue…2) In drug discovery several methods like bioassay ,high through put screening(High throughput screening (HTS) is the use of automated equipment to rapidly test thousands to millions of samples for biological activity at the model organism, cellular, pathway, or molecular level )and computer based designs are used to find chemical compounds or biologics that bind that identified target. If a compound modulates the target in a way that is expected to alter the disease , this is so called hit will be refined to improve the safety and effectiveness eventually becoming a drug candidate. 22

23. BioAssay = Bio+assay Bio=Living body,Assay =to test and analyse Procedure to estimate pharmacological activity of new or chemically undefined substances, thier mode of action how the compound will be function in the body , as well as to determine side-effect profiles, including toxicity using living tissue or body(both invtro mainly as well as invivo ). 23

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26. 26 The results of HTS assays provide hence the starting point for further steps in the drug discovery pipeline like drug design, and for understanding the interaction or role of a particular biochemical process. Consequently, high-throughput screening should be seen as a fast scan of biological processes by which compounds with a poor or no effect can be rapidly excluded from the analysis pipeline.

27. Hit to lead  ( H2L ) also known as  lead generation  is a stage in early  drug discovery  where  small molecule  hits from a  high throughput screen  (HTS) are evaluated and undergo limited optimization to identify promising  lead compounds .These lead compounds undergo more extensive optimization in a subsequent step of drug discovery called  lead optimization  (LO). [3][4]  The drug discovery process generally follows the following path that includes a hit to lead stage: Target validation (TV) → Assay development →  High-throughput screening  (HTS) → Hit to lead (H2L) →  Lead optimization  (LO) →  Preclinical development  →  Clinical development The hit to lead stage starts with confirmation and evaluation of the initial screening hits and is followed by synthesis of  analogs  (hit expansion). Typically the initial screening hits display  binding affinities  for their  biological target  in the micromolar (10 −6   molar concentration ) range. Through limited H2L optimization, the affinities of the hits are often improved by several orders of magnitude to the nanomolar (10 −9  M) range. The hits also undergo limited optimization to improve  metabolic half life  so that the compounds can be tested in  animal models  of disease and also to improve  selectivity  against other  biological targets  binding that may result in undesirable side effects. On average, only one in every 5,000 compounds that enters  drug discovery  to the stage of  preclinical development  becomes an approved drug 27

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31. Step 4: Early Safety Tests on promising compounds Lead compounds go through a series of tests to provide an early assessment of the safety of the lead compound. Scientists test Absorption, Distribution, Metabolism, Excretion and Toxicological ( ADME/Toxicity) properties, or “pharmacokinetics,” of each lead based on invivo and invitro as well as animal models.basically starts the preclincal steps Successful drugs must be: 1. absorbed into the bloodstream, 2 distributed to the proper site of action in the body, 3 metabolized efficiently and effectively, 4 successfully excreted from the body and 5 demonstrated to be not toxic. Hey help in identifying the toxicity or any lethat effecs and eliminate them by doing structural modications . These studies help researchers prioritize lead compounds early in the discovery process. ADME/ Tox studies are performed in living cells, in animals and via computational models . 31

32. STEP 5: Lead Optimization This is nothing but altering the structure of lead candidates to improve properties Lead compounds that survive the initial screening are then “optimized,” or altered to make them more effective and safer. This process starts by confirming that a true structure-activity relationship (SAR) exists within a number of hit series for the biological target.   Hit-to-lead projects typically run for 6 – 9 months. By changing the structure of a compound, scientists can give it different properties. For example, they can make it less likely to interact with other chemical pathways in the body, thus reducing the potential for side effects. Hundreds of different variations or “analogues” of the initial leads are made and tested. This optimization is accomplished through chemical modification of the hit structure, with modifications chosen by employing knowledge of the  structure–activity relationship  (SAR) as well as structure-based design if structural information about the target is available. Teams of biologists and chemists work together closely: The biologists test the effects of analogues on biological systems while the chemists take this information to make additional alterations that are then retested by the biologists. The resulting compound is the candidate drug. 32

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34. The  structure – activity relationship  (SAR) is the  relationship  between the chemical  structure  of a molecule and its biological  activity . ... The analysis of SAR enables the determination of the chemical group responsible for evoking a target biological effect in the organism. This allows modification of the effect or the  potency  of a  bioactive compound  (typically a drug) by changing its chemical structure.  Medicinal chemists  use the techniques of  chemical synthesis  to insert new chemical groups into the biomedical compound and test the modifications for their biological effects. Structure Activity Relationships (SAR) can be used to predict biological activity from molecular structure.  This powerful technology is used in drug discovery to guide the acquisition or synthesis of desirable new compounds, as well as to further characterize existing molecules. 34

35. The biological effects of a new chemical compound can often be predicted from its molecular structure using data about other similar compounds. This is because similar compounds may have similar physical and biological properties. There is a relationship between molecular structures and their biological activity, and this principle is referred to as Structure Activity Relationship (SAR). Structure Activity Relationship is typically evaluated in a table form, called an SAR table.  SAR tables consist of the compounds, their physical properties, and activities. Experts review the table by sorting, graphing, and even scanning structural features in order to find possible relationships. The interactions of drugs with their biological counterparts are determined by intermolecular forces, i.e. by hydrophobic, polar, electrostatic, and steric interactions.  35

36. 36 Paracetamol  seems to  work  by blocking chemical messengers in the brain that tell us we have pain.  Paracetamol  also  reduces fever  by affecting the chemical messengers in an area of the brain that regulates body  temperature. Acetaminophen is a  p-aminophenol  derivative with analgesic and antipyretic activities. Although the exact mechanism through which acetaminophen exert its effects has yet to be fully determined, acetaminophen may inhibit the  nitric oxide  (NO) pathway mediated by a variety of neurotransmitter receptors including  N-methyl-D- aspartate  ( NMDA ) and  substance P , resulting in elevation of the pain threshold. The antipyretic activity may result from inhibition of prostaglandin synthesis and release in the central nervous system (CNS) and prostaglandin-mediated effects on the heat-regulating center in the anterior hypothalamus.

37. Molecular docking  is the study of how two or more  molecular  structures (e.g., drug and enzyme or  protein ) fit together Molecular docking is a kind of bioinformatic modelling which  involves the interaction of two or more molecules to give the stable adduct . ... Molecular docking generates different possible adduct structures that are ranked and grouped together using scoring function in the software 37

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39. Step 6: Pre-clinical testing This is lab and animal testing to determine if the drug is safe enough for human testing. Scientist carry out “In Vitro” (test tubes & beakers) and in vivo (cell culture/ animal models) The US-FDA requires extremely thorough testing before the candidate drug can be studied in humans. During this stage researcher also must work out how to make large enough quantities of drug for clinical trials. (this is also called scale-up for patient population). After extensive work of several years scientist screened 5K-10K compound and narrowed to 1 to 5 molecules c alled “Candidate drug” 39

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48. Pre-clinical development The pre-clinical development includes the following: develop large scale synthesis; animal safety studies; carcinogenicity tests; drug delivery; elimination and metabolism studies; drug formulation experiments; dose-ranging studies in animals. Wide ranging dosages of the compounds are introduced to the cell line or animal in order to obtain preliminary efficacy and pharmacokinetic information. 48

49. Toxicity testing of new compounds is essential for drug development process. The preclinical toxicity testing on various biological systems reveals the species-, organ- and dose- specific toxic effects of an investigational product. The toxicity of substances can be observed by (a) studying the accidental exposures to a substance (b)  in vitro  studies using cells/ cell lines (c)  in vivo  exposure on experimental animals. This review mainly focuses on the various experimental animal models and methods used for toxicity testing of substances. The pre-clinical toxicity testing helps to calculate “No Observed Adverse Effect Level” which is needed to initiate the clinical evaluation of investigational products. Toxicology is a branch of science that deals with toxins and poisons and their effects and treatment. Toxicological screening is very important for the development of new drugs and for the extension of the therapeutic potential of existing molecules. The US Food and Drug Administration (FDA) states that it is essential to screen new molecules for pharmacological activity and toxicity potential in animals 49