med chem

what are some protein protein interaction examples

cellular structure
immune response
signal transduction
apoptosis (cell death)

even though protein protein interactions don’t contain covalent bonds why are they able to have such strong ;bonds
because of the large surface areas that interacy
what is the hotspot in protein protein interactions
patches of area on the amino acid that have hydrogen bond doner/acceptor
can your inhibitor work if it does not have the same or more favorable bindining affinity as the substrate
yes if you have a higher concentration
do you need to know the entire protein structure to block binding of proteins
no you can target enzyme active sites
explain how target based drug design narrows down the library of molecules
Experimental screening (competitive binding, enzyme assay, fluorometry) and computational screening;
what is peptidomimetics
Inhibitors based on primary or secondary structure of the part of the partner protein that participate in PPIs ;(this means you will conserve the key parts)
when do you use partial atomic charges
when dealing with H bonds (accounts for the dipole moment)
why use;peptidomimetics
this is because you will have the save binding points to compete with your protein
what are some challenges for developing PPI

1.Natural small molecules known to bind at protein ; protein interfaces are rare –> no template available for designing antagonists
2.Difficult to locate small, deep cavities that could make good small-molecule binding sites from  X-ray structures
3.Assaying inhibition is difficult in contrast to enzyme inhibition (recall Michaelis-Menten: competitive vs. allosteric antagonists of enzyme activity)
4.Therapeutic antibodies although effective (e.g. Herceptin), are not cell-permeable and so cannot be given orally
5.“Hot spots” appear to have conformational flexibility, and can adapt from a near-flat surface to a cavity capable of binding a small molecule.

why is ERK a great target for drug design

nActive in cell proliferation in many types of cancers
nCrystal structures of the active and inactive form are available
nMutagenesis studies have discovered residues important for binding to its substrates (blue and green)

how does signal transduction relate to drug design
 this is typically a good target for PPI inhibitors
what is HCK
a non receptor tyrosine kinase that is part of a signal transduction pathway for cell proliferation
what are the targets for PPI

transcription factors (BCl6 in cancer)

signal transduction pathways ( Erk of the mitogen pathway,

and HCK of the SRC family

why target DNA transcription factors for PPI
cancer has a misregulation of these
what are two important methods of developing inhibitors of protein protien interactions

target based


what is the first protein based drug
in 1977 we cloned somatostatin what is this called
genetic engineering
what is erythropoietin

i ) Kidney glycoprotein that stimulates growth of red blood cells in bone marrow
ii) Approximately equal mass of protein (34
kD) and carbohydrate
iii) Used in anemia
iv) Abused by athletes

what are some examples of biotech drugs


blood factors

growth factors

human growth hormone


enzymes (adenosine deaminase


describe what human growth hormone is

i) From pituitary gland, used for growth deficiencies in children (nanism, dwarfism)
ii) Hormone originally isolated from human cadaver pituitary (Creutzfeldt-Jakob syndrome)

what is somatotropin
this will cause the release of human growth hormone
explain what cytokines are produced as a drug

i) Interleukins (ILs)
    a) Immune system hormones
    b) Interleukin-11 (rhIL-11,
oprelvekin, Neumega, Genetics Institue) for treatment of Chemotherapy induced Thrombocytopenia

     ii) Interferons

          a) Generally antiviral, antiproliferative and immunomodulatory effects.
    b) Interferon Beta-1A and 1B: used in treatment of relapsing multiple sclerosis

what are the issues with protein based drugs

1) Antigenicity (non self vs self)

2) Stability

3) Drug Delivery

the protein needs to have the appropriate 3D structure

how do we get around antigeneicity in MABs

i) chimeric antibodies
    ii) antibodies produced in transgenic mice, rats or yeast

        iii) phage display antibodies

what contributes o instability in protein drugs

   deamidation: Asn, Gln

   oxidation: Met

   proteolysis: Arg, Lys

   racemization and acid labile: Asp

   disulfide exchange: Cys, disulfide

   aminolysis: Lys

   beta-elimination: Cys, Ser, Thr, Lys

b) Proteolysis during storage due to enzymes associated with bacterial contamination

how can you help preserve protein drugs

c) Protein often more stable in dry form (lyophilized)

d) Additives to enhance stability

e) Detection of instability

what methods do you use to measure the stability of a recombinant protein

  1. SDS page-detecs frafmentation, crosslinking, oligomerization
  2. RP-HPLC- deamidation, crosslinking, methionin oxidation, disulfide scrambling
  3. IEF- deamidiation
  4. potency determination- disulfide scrambline (most important)

what are some issues with drug delivery of protein drugs

hard to give without denaturation (chemical alteration)

rapid liver clearance

what are some solutions to drug delivery pproblems with protein based drugs
give drugs parenterally, nasal, implants, use microspheres for sustained release, inhalers
what kind of changes would you see in a 2nd generation protein based drug
      i) Modification or removal of selected amino
      ii) Production via an alternate source (see below)
      iii) Deletion of unessential portion of the protein (e.g.
      iv) Introduction of disulfide bonds
      v) Proper phosphorylation required for biological activity
what will maintain a proteins 3d structure when it is dried out
glycosylation (sugars)
what receptor recognizes the carbs on the surface of a protein
asialoglycoprotein receptor (basically there to replace damaged proteins)
why would you pegylate your protein
this should decrease clearance and thus increase efficacy
what are some sources of protein products



mammalian cells

transgenic animal/ plant sources


what are some charecterisitcs of using E.coli to produce your proteins

i) Cheapest
ii) No glycosylation or
disulphide formation
iii) Fusion proteins

      iv) Met at N terminus of the
v) Toxins (gram positive bacteria) in

what are some charecteristics of using yeast to make your proteins

i) Relatively inexpensive
ii) Hyper or incorrectly glycosylates

      iii) Correct disulfides 
iv) No toxins
v) Proteins excreted into medium

what are some charecteristics of using mammalian cells to produces your proteins

i) Most expensive of cell-based methods
ii) Produces the most active protein due to proper modifications
iii) Proper post-translational modifications

propeptide processing

what is the deal with using transgenic animals as a source for proteins
insert a gene so that the animal will express the protein of interest and maybe secrete it in it’s milk or egg
in a protein based durg is it easier to prove bioequivelance
no since you have very subtle changes in production that alter bioequivelance
what does an antisense oligodeoxynucleotide do
it binds to the DNA strand to block expression of the protein
what is the difference betweent antisense and sens agents
antisense you only need to develop a 1 dimensional drug (know the sequence of the DNA) where as in sens you need a particular 3-d structure
if you increase the length of an antisens agent what increases and what decrease

affinity increases (and your able to miss a pair)

you decrease specificity

what is the magic number to max affinity before you lose specificty
15 base pairs
in a antisense agent what type of base pairs will increase affinity
what are some antisense targets

Target genes at DNA or RNA level that code for

     i) proteins in microorganisms to kill invading organism

     ii) proteins specific to cancer

     iii) any undesired protein

in leukemia how can use antisense agents

remove the bad bone marrow and replace it with good bone marrow

kill the leukemia cells in the bone marrow

how does an antisense agent work at the DNA level

blocks transcription by forming a triplex (three strands)

 works at single strand to form a bubble

how is the antisense agent going to work on the mRNA level

during synthesis

at the intron exon junction

inhibits protein initiation factors

how does an antisense agetn work to block ribosome interactions

at the start codon

and overall interactions

what are some issues with antisens development

absorption (limited ability to cross membaranes


affinity to binding

how can you enhance antisense products uptake

co-admin with cationic lipids

encapsulation in carbs

chimeric molecules

alternate backbones (with methylphosphonate)

how can you increase stability of antisense products

block 3 prime exonuclease activity

sub the phosphodiesterase bond with a peptide bond


what kind of sugar modifications can you make to antisense molecules

i) Enhance stability and affinity: alphaanomer at 1′ position of 2’deoxyribose

     ii) Resistance to nucleases: 2-OH modifications of ribose including 2’methyl,  2′-allyl, or 2′-fluoro (also enhance affinity)

what kind of base modifications can you make to your antisense molecules

Hydrophobic modifications of 5′ position of pyrimidines that enhance affinity for target RNA or DNA

what is interference RNA
a molecule that forms a duplex of with mRNA then it degrades it (this ultimately causes gene silencing)
how do they deliver interference RNA
give it a short hairpin then once it gets into cell the dicer will cut it up
what is a ribozyme
RNA molecules that assume tertiary structures and have the ability to catalyze chemical reactions, making them catalysts
what are some applications of ribozymes

target HIV

and lower expression  of MDR (transporters that eject drug from cell)

what are goals of target based drug design

1) Understand atomic details of drug binding strength and specificity

2) Identify or create novel molecules to bind to a selected target and elicit a biological response via de novo drug design or database searching techniques

3) Optimize the therapeutic index of an already available drug or lead compound

what stabilizes a beta sheet 
the bond between the carbonyl and the NH group
where can you find a prosthetic group
in vitamins (tertiary structure)
what kind or receptor is rhodpsin
G-protein coupled receptor
what is molecular modeling

3D representation of molecules based on graphic or mathematical representations of chemical structures

what is quantum mechanics

treat electrons explicitly

limited to 100 atoms

what is molecular mechanics

deals with atom as smallest particle

every atom interacts with ever other atom

allos you to study a system with millions of atoms

what is the empiracal energy finction

V total=Vinternal+Vexternal

where Vinternal=Vbonds+Vangles+Vdihedrals


what is dihedral angle talking about
rotation about the central bond
when looking at the COS function for a dihedral bond how can you tell the difference between a single bond and double bond

double bond has 2 peaks (a peakseperated by 180 degrees)

in a single bond you have 4 peaks (each peak seperated by 60 degrees)

when looking at the van der waals energy diagram what happens to attractive forces and repulsive foces

the closer you get the less your attractive forces are

the closer you are the greater your repulsive forces

for a double bond how many maxima and minima are there
if a molecules graph (dihedral angle vs potential energy goes to 0 at 0 degreess and 360 how many global minima are there
what is energy minimization
figuring out how to alter your structure to get to the lowest energy level (must go from energy to force)
what happens to force the further away from the minima you are
the more posative or negative it becomes
how do you figure out how many degrees of freedom you have
the amoung of conformations raised to the power of the amount of atoms are in the molecule
how long can you predict movement in an atom of a molecule
fentos second (10to the -15S)
MD simulations can give you what values
entropy but ultimately free energy
what info is required for calculations of energy for minimization and for molecular dynamics

energy (atom positions)

energy minimizations (atoms positions, forces)

molecular dynamic simulation (atom simulation, forces, atomic velocities)

what id docking (database searching)
screening through a list of none compounds to see if they will bind to your site
what is de novo design
design novel compounds by putting diffrent pieces together to fit your recteptor
what is pharmacophore

geometric arrangment of functional groups

can be determined by 3d structure, knowledge of ligand

what is grid in relation to pharmacophore

this is a way to develop a pharmacophore by

a) Prepare a 3D lattice of grid points encompassing the binding site

b) Determine interaction energy of different types of functional groups with binding site at each grid point.


c) Select favorable interaction sites


d) Determine relative spatial orientations of the selected interaction sites

in a grid what yields a pharmacophore
types of functional groups and their positions
what counter acts a dipole
solvation energy this may facot for example a carbonyle
explain what docking is
Computationally identify compounds with a high probability of binding to a site on a protein or RNA
what are the steps in docking

  1. determine solvent accessible surface of binding pocket (spheres)
  2. generate a negative image of receptor based on spheres
  3. determin sphere distances of the negative image
  4. convert sphere distances to atom distances
  5. compare atom distances with actual atom distances
  6. select ligands with greatest overlap
  7. calculate ligand receptor interaction energies

what is groupbuild
this is a de novo computer program that builds a molecule up from scratch to the receptor
how do you perform a group build

  1. develop a grid for binding site (include electrostatic, VDW)
  2. generate a structures (first is the core, then you build up on it then randomly select one of the top 25%
  3. synethesise compounds

how do analyse yo’u groupbuilt structure

A)Visual examination of structures for chemical feasibility

B) Identify specific positions of certain functional groups etc. that my be related to a known pharmacophore

C) Database screening for similar compounds in chemical databases (avoid synthesis!).

what are the limitations of database screening and de novo design


Rigid geometry of receptor and ligand

  Ligands often treated as flexible

  Multiple conformations of receptor can partially overcome rigid representation

Inherent assumptions and simplifications in molecular mechanics


how do you perform lead compound optimization
use free energy perturbation 
what are the steps involved in drug receptor interactions

1) diffusion controlled encounter

2) initial Michaelis complex

3) desolvation of both inhibitor and binding site

4) conformational changes of both inhibitor and binding site upon binding

5) correct orientation between drug and receptor binding site

what is Thermodynamic cycle applied to relative binding of two inhibitors

a method to compare 1 drug receptor complex to another


how is alchemical perturbation performed

  1. in a computer you change molcule 1 that is bound to the receptor to molecule 2 in the receptor
  2. this is done by change the equilibrium and force constants in small steps

why perform alchemical perturbation since in reality you can’t do it
since you can just develop the final product (the final state is the only thing that matters)
how does free enery component analysis work
you will essentially add up all the portions that contribute to the whole
Dihydrofolate Reductase is a target for drugs why
it is involved in synthesis of DNA and can be a target to stop cancer
what diseases are Dihydrofolate Reductase targets involved in

1) Anticancer agents

2) Antibacterials

3) Non-surgical abortions

Dihydrofolate Reductase uses what as an electron source

what makes up Dihydrofolate Reductase, and which are good targets for drugs

glutamic acid

benzoic acid



the drug target is the pteridyl

what are the three different types of Dihydrofolate Reductase inhibitors

  1. amino pteridine (competative inhibitor)
  2. methotrexate (just adds a cabonyl to the amino group of the pteridyl )
  3. trimethoprim

why use natural products

  • we evolved with them
  • chemistry is similiar
  • diverse plants and diverse chmistry as a result
  • tend to be nourshing and supportive

what is the doctrine of signature

using a plant that mimics human anatomy or disease



Walnut for brain health •

Red juice of bloodwort for blood disorders •

Kidney-shape leaves of Hepatica to treat  •

kidney disease

why eat organs
some cultures believe that eating an organ will give you a healthy organ kidney for enhanced kidney
what were some other uses of natural producte

  1. arrow poison
  2. religous rituals (phyostigma
  3. belladonna oracle of apollo, and cosmetics
  4. as corecers drug


traditional chinese med started by shen nung used what

wormwood against malaria, fever

toad skin for heart conditions (digitalis glycosides)

used ephedra sinica as stimulant

what is pen tsao kang mu
this is a book of chinese traditional meds compiled in the ming dunasty
what is the ebers papyrus

16th century book on its meds


what are some herbals that were dated back to egypt
aloe and poppy seeds
where was snake root used first
what laid the foundation of western medicine
ancient greeks (hippocrates esp)
what is de materia medica
this was a compliation by roman dioscorides that had over 600 species of plants with medical values
whats the deal with mandrake
it was used as a pain killer anesthatic
how did islam contribute to medicine
pharmacy had the highest reputation in arab world, and was the first time it was independent
where was the fist pharmacy
baghdad in 8th centurary
what is hindiba
a plant to treat cancer
what is black seed

regarded as the greatest form of healing med in islam

now it is none to have many of the nutrients reccomended by the FDA

the start of the renasissance rang in
the age of herbals
how many americans use CAM

40% of american population

73% of cancer patients

what is the largest part of CAM

herbal medicine




what is the problem with herbals branded as supplements

labeling issues

no quality control

misinformation in literature

are herbal meds standarized (guranteed to have certain amount of active ingredient)
some are some are not
what are the top three challenegs with herbal products

supply issue

quality issue

safety issue (herbal drug food interactions)

thermogenics are herbs to control weight loss what is the most common


followed by ephedra

what is nother name for ephedra
brigham tea
what is fo-ti root

long life elixer

reverses gray hair, ED, vaginal discharge

research on fo-ti root revealed what

it may lower cholesterol

mild laxative

what is bay chi root supposed to do
be an antioxident lower blood pressure
what is konjac used for
reduce appetite, regulate insulin, help with weight, regulate LDL cholesterol
what can apple cider vinegar do for you

weight loss

lower blood pressure

reduce cholesterol

fight arthritis pain

relief sore throat

glucosamine is safe for regular use for how long
4 years
what is SAMe used for
depression arthritis liver disease heart disease
what are the top ten herbals





soy bean

saw palmetto

st john’s wort



black cohosh

what is active ingredient in ginko and is effective for what

increase blood flow

possibly effective in dementias

only safe for a year use

when should you not use ginko
with caffeine and stimulants, with antiplatelets
what does echinacea do for you

produces nonspecefic immune activation

use with flu

how long can you use echinacea for

12 weeks

8 weeks in autoimmune disease

why not use long term
can be immunosupprsive and in autoimmune disease will exacerbate symptos
what is garlic used for

active ingredient allicin will lower lipids and cholesterol


how should you take garlic
enteric coated since it will be destroyed by gastric acid
what is ginsing used for
possibly effective for improved cognitive function, type 2 DM, bronchitis
how should you use ginsing (how long)
3 months on and a period off
what are some interactions of ginsing and precautions

interacts with lasix, inhibit barbitutes

may increase BP and overuse can give insomnia headaches etc..

what is soybean used for
estrogen replacement
what is saw palmetto used for
helps relieve stage 1 and 2 BPH due to anti-teterterone action
what can you use st. johns wort for
may work on mild to moderate depression
what are some contraindications to st johns wort

sever depression, suicidal tendencies, sever agitation, prego, may induce seratonin syndrome with triptans, mat interfere with cyclosporin, inhibits CYP450

may cause photosensitvity

what do you use valerian for
sleep sedation
what is black cohosh used for
relieved premenstrual symptoms
what is milk thistle used for
used to help chronic liver disorders
what is ginger used for
anti emetic antimotion sickeness
what percentage of drugs are derived from natural products

about 25%

74% of anticancers

78% of anti-bacterial

why has natural products for drugs been on the decline
 incompatablity with HTS
what are natural products as drug sources

natural products produced in cells

primary metabolites

secondary metoblites

what are lipinski’s rule of 5 for oral drugs



  1. Not more than  ?5 H bond doners (OH and NH groups) 
  2. hydrogen bond acceptors  10 (5X2) Not more than (notably N and O) 
  3. A molecular weight under 500 (5×100)  ?
  4.   A partition coefficient logP 5 under
  5. < then 10 rotatable bonds



what are the three most common toxic substances within herbals

pyrrolizidine alkaloids

phorbal esters

aristolochic acids

what is wrong with BOrage

it can be teratogenic, carcinogenic, hepatoxic

contains pyrrolizodine alkaloids

what is wrong with sweet flag
contains cis-isoasarone that is a carcinogen
what is wrong with chaparral

is nephrotoxic and hepatotoxic

contains NDGA

what is wrong with coltsfoot
hepatotoxic pyrrolizidine alkaloids
what is wrong with comfrey
this is hepatotoxic due to pyrrolizadine alkaloids
what is wrong with germander
 hepatotoxic due to diterpenoids
what is wrong with licorice

it is a pseudoaldosteronism (retains Na, water and depletes K)

this is dose dependent

what is wrong with poke root
this is highly toxic to organs due to triterpenoid saponins
what is wronge with sassafras
contains safrole which is a carcinogen
rule of thumb for herbals

 Avoid using herbs in 

infants, children, pregnant women, 

nursing mothers, patients w/ daisy 

allergies, patients on multiple 


herbals can effect drugs how

they can alter transporters

they can alter CYPS

alter absorption

compete with drug targets

what drug interacted with saquinavir
how does St.Johns wort affect CYPD3A4
it will induce it
what are the applications of QSAR


diagnosis of mechanisms of drug action

prediction of activity (in congeneric series)

lead compound optimization

how did we make sulmazole stop giving us halucinations
used QSAR to do a bio-isoteric replacement lowreing coefficient to 1.2 so it dind’t cross BBB
what is the hammemett electronic parameter (σ)
this will tell you the electron donatin or withdrawing properties
what does a positive σ tell you
that you have an electron withdrawing group and increase Ka
what does a negative σ
it is electron donating  and it will decrease Ka
when you substitute at the para position how will this effect the ring, how about ortho and meta

  1. the ortho position will have minimal transferability
  2. the meta position will have an inductive effect (may favor unionized thus smaller Ka) a -σ
  3. if you have a para substituant then you will have resonance effects(increasing Ka) a +σ

what is the general utility of σ values
it allows you to predict it’s value and contribution for similiar compounds
when graphing σ what is a posative slope and a negative slope

the posative slope is an electron withdrawing group

the negative group is electron donating

what is tafts seric parameter


this says that the impact of the substiuant is dependent on size( the term is always negative and the more so it is the more steric hinderance)

what does molar refractivity tell you
the molar refractivity goes down as the molecule becomes more dense and this is better
how can we apply QSAR to the biologic system (biological hammet relationship)

Consideration of need to cross membranes

Blood brain barrier

Lipophilicity (hydrophobicity)-this will dictate how fast it can cross the barrier

what is the hydrophobicity

if it is + then it will be more hydrophobic

if it is- it will be more hydrophillic

say you have a functional group that adds a ∏ of.5 and the same thing next to it how would you calculate the overall effect
.5+.5+interaction factor
when you use the linear equation you will have a final K what is this
this the activity of the unsubstituted compound
if you want to increase activity what do you want ∏ to be and σ

  1. ∏ you will want this to be negative, but not so much to where it wont go into the lipid bilayer (more hydrophillic)
  2. σ you will want this to be posative (electron withdrawing)

what is the disadvantage of hansch equation

hard to extrapolate byond your list

predictions are limited to rings

you will need 5 compounds for every term you use

what is the spanned substituion space
range of physical properties covered by the compounds in the training set (QSAR)
the free wilson model tells you what

it’s like an on off switch

I is substituant and J is location

what is the topliss decision tree

  • basically trying to find your drug without using a training set
  • measure then add what you think is needed measure then keep doing this till you are close to what you want

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