What is the difference between Drugs and chemical probes?

The Basic Difference between Drugs and Chemical Probes

Drugs:Clinical approved chemical substance, which is used to treat diseases and disorders.

Chemical Probes: A chemical substance, which is used to interrogate the unsolved biological problems in order to understand them.

Chemical Probes Applications: Biological target identification, target visualization, target validation, cellular pathway identification, and identification of off target effects.

Generally chemical probes consist three regions

Fig.1 Chemical Probe

1). Reactive group (or) war head: which is generally act as an electrophile in order to trap a biological nucleophile (thiol, amine, hydroxyl groups in proteins).

2). Spacer (or) Linker: which is generally connects, two units and also enables the cell permeability e.g. peptide chain, poly ethylene glycol chain.

3). Reporter tags: again 3 types based on chemical biology application

a). Fluorescent tag: which is generally report the biological information by visualization method e.g. Indocyanine green by fluorescent microscopy.

b). Radioactive tag: Which is reports the biological distribution of a chemical compound in a particular region e.g. cell or tissue by imaging systems such as PET, SPECT scans.

c). Affinity tag: which is generally used to isolate the particular targeted protein by Biotin-Avidin affinity chromatography.

Table 1: Difference between drug and chemical probe

Drugs	Chemical probes
Has to fulfill PK&PD	Not necessary
Most of the times single purpose only	Multipurpose
Treat to disease	Disease identification and also reveals nature of target
Phenotype outcome is necessary	Not necessary
Most of the time bind with target reversibly	Most of the time bind with target irreversibly (covalent inhibitor)
Clinical trials essential	Not essential
Not toxic but sometimes show side effects	Might be toxic because of covalent nature
Clinical purpose	Biological investigation purpose

For further reading please find some useful articles below:

The art of the chemical probe URL

Rethinking screening URL

Chemical probes for biological systems URL

Prodrugs

Prodrugs are inactive form of drugs, which are readily cleavable into active form of the drug under biological environment.

Fig. A pictorial representation of prodrug concept

A prodrug is designed to pass over barrier or barriers (For e.g., Gastro Intestinal Tract (GIT), Blood Brain Barriers (BBB)) utilizing through a chemical approach rather than a formulation approach. Therefore, it is an alternative to the redesign of the cleavable drug molecule. Prodrug concept mainly deals with three main objectives such as Pharmaceuticals, Pharmacokinetics and Pharmacodynamics.

Pharmaceutical benefits of prodrug

1. A prodrug approach actually enhance the bio availability of the parent drug by increasing its permeability through cell barriers.
2. Prodrug approach increases the solubility for poorly soluble drugs
3. Prodrug approach even it is also increases the stability of less stable drugs under biological condition
4. Prodrug can act as a drug vehicle to bring the drugs to specific areas of the body parts (target specific drug delivery)
5. Prodrug approach controls release dosage form of drug for short biological half-lives containing drugs (sustain release)
6. Prodrug approach enhance patient acceptance by enhancing pleasant taste or odor of active drug 
7. Prodrug approach reduce off target effects (decrease toxic effects) of an active drug 

Prodrugs classification

Prodrugs classified into two types based on carriers attached to the drug and drug derivatization. such as 

1) Carrier linked prodrugs: In which Pro linker covalently bound to the active drug but it readily cleaved by enzymes or non-enzymatically into parent active drug. These pro linkers are inactive, nontoxic and non-immunogenic.

Carrier linked prodrugs again sub divided into 2 types

a) Bipartite: In which one carrier directly attached to the drug

b) Tripartite: In which drug connected to linker through a spacer because in some cases drug directly connected to linker is unstable.

c) Mutual prodrugs: In which two drugs linked together using a linker

2) Bio precursors: In which no carrier or linker attached to a compound but normal compound readily metabolized under particular biological environment (cytochrome P450) to active drug.

Conclusion

Prodrugs can improve ADME properties i.e pharmacokinetics of drug molecule. The basic concept of prodrug approach is to maximize the bioavailability of active drug that reaches its site of action, the carrier of prodrug that will be removed by either enzymatic or chemical transformation. These bio cleavable prodrugs are target selective without losing effectiveness of parent drug.  

undoubtedly prodrugs playing major role in drug discovery and development process by overcoming pharmacokinetics properties. 

Further Reading

You can get more information regarding prodrugs from below given URL & PDFs link


1) Prodrugs: challenges and rewards URL link
2) Prodrug Design to Improve Pharmacokinetic and Drug Delivery Properties: Challenges to the Discovery Scientists URL link

Lipinski’s Rules

Lipinski’s Rule of Five

Christopher Lipinski’s rule of five analysis helped to raise awareness in scientific community about molecular properties that make molecules more or less drug-likeness. The rules of thumb were quickly adopted as it aided to apply absorption, distribution, metabolism and excretion (ADME) considerations early in preclinical developments and also could help to avoid preclinical and clinical failure.

Lipinski’ rule extension

In attempt to improve the predictions of drug likeness, the rules lead to many extensions and those are given below point-wise

• Partition coefficient log P  ranged from  -0.4 to +5.6
• Molar refractivity ranged from 40 to 130
• Molecular weight ranged from 180 to 500
• Number of atoms ranged from 20 to 70 (H-bond acceptors and H-bond donors)
• Polar surface area no greater than 140 Ų

In addition to that the 500 molecular weight cut-off has been uncertain. Polar surface area and the number of rotable bonds has been found to better discriminate between compounds that are orally active and those that are not for a large data set of compounds in the rat. In particular, compounds which meet only the 2 criteria of:

• 10 or fewer rotatable bonds
• Polar surface area equal to or less than 140 Å² are predicted to have good oral bio-availability.

Finally Lipniski’s fifth rule effectively states that the first four rules do not apply to any molecule if that is recognizing by an active transport system, when considering “druggable chemical entities”.

Tuberculosis (TB)

Tuberculosis (TB) 

Tuberculosis (TB) is a deadly disease pandemic caused by Mycobacterium tubercle bacillus Gram positive bacteria that most often affect the lungs.

• Mycobacterium tuberculosis has an unusual, high lipid content cell wall (mycolic acid), which makes the cells impermeable to Gram staining, hence Ziehl-Neelsen stain/acid-fast detection techniques are used instead. 

• Mycobacterium tubercle needs high levels of oxygen in order to survive, so it primarily takes shelter in mammalian respiratory system and infects the lungs. 

• The incidence of this disease directly related to dense population, poverty, malnutrition and poor hygienic conditions.  

• Recently increasing emergence of drug-resistant TB, especially multidrug-resistant (at least two of first line drugs such as isoniazid and rifampin) is particularly alarming due to impermeability of the highly hydrophobic cell envelope to many drugs, as well as development of bacterial efflux pump system and production of certain enzymes to inactivate the drugs (β-lactamases, amino glycoside acyl transferase). 

• The lethal combination of drug-resistant TB and HIV co-infection is a growing problem in TB control. 

• Multidrug-resistant tuberculosis leads to extensively drug-resistant TB (XDR TB) due to irregular medication and mismanagement of all prescribed medicines. XDR TB is resistant to isoniazid and rifampin, plus at least one of the three injectable second-line drugs (amikacin, kanamycin, or capreomycin). 

TB therapy

• Single drug treatment in tuberculosis resulted in the rapid development of resistance and treatment failure. 

• According to various experimental and clinical studies by WHO recommended standard TB chemotherapy, called DOTS (directly observed treatment, short course), is a combination six months therapy comprising of an initial two-month phase of treatment with four drugs such as isoniazid (INH), rifampicin (RIF), pyrazinamide (PZA) and ethambutol (EMB), followed by a continuation phase of treatment with INH and RIF for another four months.

• It has a cure rate up to 95%. However, DOTS alone may not work in areas, where there is a high prevalence of MDR-TB. In such situations, WHO recommends the use of DOTS-Plus.

•  The current TB drugs categorized as first-line drugs (ethambutol, isoniazid, pyrazinamide, and rifampicin), second-line drugs (amino glycosides, polypeptides, fluoroquinolones, thioamides, cycloserine, terizidone) and third-line drugs (rifabutin, macrolides, linezolid, thioacetazone, thioridazine, arginine, vitamin D, R207910). 

Classification of TB drugs based on mechanism of action

TB drugs are classified into four groups based on mechanism of action. 

a) cell wall synthesis inhibitors (INH)

 b) nucleic acid synthesis inhibitors (RIF, FQ)

c) protein synthesis inhibitors (SM)

d) Membrane energy inhibitors (PZA)

Traditional Chinese Medicine (TCM): Importance in Drug Discovery

TCM is established on a patient's current state of yin and yang, four natures, five tastes and the meridians. In the Four Natures, each herb has a quality of hot or cold (yin/yang) associated with it, in which it can be used to balance out a person's own yin/yang state. The Five Tastes consist of sweet, sour, bitter, salty and pungent, each of which has its own set of features and effects.

The folkloric uses of CMM (Chinese Meteria Medica) have led to many instances of corresponding successful drug development; some of them are listed in below Table.

S.NO	Plant source	Chemical compound	Disease treated/use
1.	Ephedra sinica	(-)-Ephedrine	Bronchodilator
		Pseudoephedrine	Decongestant
2.	Indigo naturalis	Indirubin	Chronic myeloctyic leukaemia
3.	Artemisia annua	Artemisinin	Malaria fever
4.	Podophyllum pelatum	Podophyllotoxin	Anticancer
5.	Euphorbia kansui	Kansuiphorins A	Ascites and cancer
6.	Salvia miltiorrhiza	Tanshinone II-A	Angina pectoris and myocardial infarction
7.	Brucea javanica	Brusatol	Antileukemic activity
8.	Panax ginseng	Protopanaxadiol	Anticancer activity

Traditional Indian System of Medicine (ISM): Importance in Drug Discovery

Ayurveda-the science and knowledge of life, is acknowledged as a lifestyle in itself since it is a three-dimensional healing system and explains how the interaction between body, mind and spirit can be predicted, balanced and improved to enable us to stay or become healthy and vigorous. This traditional medical practice consists of leading a life in which the body, mind and spirit are in harmony with one another, and asserts that if this harmony is disrupted, the imbalance will make it difficult to sustain a healthy life. According to the survey carried out by the department of AYUSH, Ayurveda remains a major traditional medicine for most of the people (65%) in India.  As seen from bar diagram which depicts the System-wide distribution of AYUSH licensed pharmacy as on 1.4.2008, Ayurveda’s share of licensing constitutes 86% of the total licenses issued by AYUSH (Source: Report of 11th year plan of AYUSH).

A large number of promising lead molecules that have come out of Ayurveda are listed in Table and include some of the most important drugs that are in vogue in the present times such as Reserpine, L-Dopa, CNB-001, Colforsin Daropate etc.

S.NO	Plant source	Chemical compound	Disease treated/use
1.	Cinchona officinalis	Quinine	Malaria
2.	Rauwolfia serpentina	Reserpine	Hypertension & tranquilizer
3.	Psoralea corylifolia	Psoralens(development PUVA for psoriasis)	Vitiligo & psoriasis
4.	Wrightia antidysenterica	Holarrhena alkaloids (conessine)	Amoebiasis
5.	Commiphora wightii	Guggulsterons	Hypolipidemic agents
6.	Mucuna pruriens	L-DOPA	Parkinson’s disease
7.	Piper nigrum	Piperidines	Bioavailability enhancers
8.	Bacopa monnieri	Baccosides	Mental retention
9.	Picrorhiza kurroa	Picrosides (Apocynin)	Hepatic protection & Bronchial asthma
10.	Phyllanthus emblica	Phyllanthins	Antivirals
11.	Curcuma longa	Curcumines(development of CNB-001 for ischemic stroke)	Inflammation
12.	Withania somnifera	Withanolides (Sensoril®)	Immunomodulators/Schizophrenia
13.	Dysoxylum malabaricum	Rohitukine (development of synthetic analog Flavopiridol)	Chronic lymphocytic leukemia
14.	Plectranthus barbatus	Forskolin (development of semisynthetic analog Colforsin daropate)	Obesity and atherosclerosis
15.	Berberis aristata	Berberine alkaloids	Anti-dyslipidemia

Natural Products Chemical Modification: Importance in Drug Discovery (Part-II)

Chemical modification of morphine led to heroin (potent opioid analgesic by increasing blood brain barrier permeability), codeine (antitussive), Apo morphine (erectile dysfunction and Parkinson’s disease), hydromorphone (potent analgesic drug).

Similarly modification of Thebaine led to thebacon (Acedicon™ antitussive), oxycodone (narcotic analgesic), etorphine (analgesic 1,000-3,000 times more potent than morphine generally it used to immobilize elephants or large mammals), oxymorphone (opana®, powerful opioid analgesic), buprenorphine (treat to opioid addiction), oxymorphol (analgesic and antitussive).

Khellin was initially used as bronchodilator but found to cause nausea and vomiting. Chemical modification of Khellin led to chromolyn (used as sodium chromoglycate), which enabled the drug to stabilize cell membrane in the lungs to prevent the allergen induced release of substance ultimately seen as a cause for bronchoconstriction in allergic asthma patients.

Similarly, modification of natural product papaverine led to verapramil a drug to treat hypertension. Galegine isolated from Galega officinalis provided template for the synthesis of Metformin an anti-diabetic drug. Similarly clinical utility of podophyllotoxin as an antitumor agent largely have been abandoned because of its side effects like gastrointestinal toxicity and poor water solubility. However, structural modification led to development of new semisynthetic glucoconjugate analogues Etoposide, Teniposide. Salvinorin A (Salvia divinorum Mexican plant) is a hallucinogen, structural modification led to 2-ethoxymethyl salvinorin B (10 times stronger than salvinorin A), Herkinorin reduced kappa opiod action and instead act as µ-opioid receptor agonist. Another example of structural modification is development of prodrug Minnelide from Triptolide, developmet of CNB-001 from curcumin and development of colforsin from forskolin. Structural modification of Hesperdin (citrus fruit) to the development of diosmin for venous disease (chronic venous insufficiency), structural modification of Amygdalin to the development of Laetrile, structural modification of parthenolide led to development of dimethyl amino parthenolide, melampomagnolide B. In addition to that structural modification of thapsigargin led to the development of G-202 and structural modification of illudin S led to development of irofulven.

Despite of natural product modification, natural product mimics also contributed to drug discovery. Based on the observation that a nonapeptide (Glu-Try-Pro-Arg-Pro-Glu-Iie-Pro-Pro) from Viper venom caused lowering of blood pressure, new hypertensive agents were developed which are known by trade name “Prils” like Captopril, Enalapril, Lisinopril, Cilazapril, Spirapril. These constitute one of the most important classes of cardiovascular drugs. Likewise, drugs have been developed which involve synthetic molecules/materials from agents originally derived from plants. For example, Psuedoephedrine, originally derived from Ephedra sp., has been a model for the preparation of new synthetic drugs like Propronalol, Metaprolol, Atenolol, and development of Docetaxel from Paclitaxel, development of Navelbine (Vinorelbine) from Vinblastine, Flavopiridol from Rohitukine, Carfilzomib from Epoxomicin, Ivermectin from avermectin etc. The above example proves clearly that the structural modification of natural products has a greater role in Drug Discovery.