Archive for Sci Update

Amide Coupling in Medicinal Chemistry

In recent years, amide coupling has become the most frequently used reaction in medicinal chemistry1.  Found as the backbone of proteins, the amide bond is nominal formed by the condensation of a carboxylic acid and an amine.  Due to a nearly unlimited set of readily available carboxylic acid and amine derivatives, amide coupling strategies can be an efficient approach for medicinal chemists to generate novel compounds.  As a result of this utility, a nearly unlimited set of reagents and protocols have been development to afford this simple transformation of amide bond formation2,3.

Amide Bond Formation


The most common method for formation of an amide bond is the condensation of a carboxylic acid and an amine.  Generally, the carboxylic acid needs to be activated in order to react with the amine while remaining reactive functional groups need to be protected.  This process occurs in two steps in either one pot with direct reaction of the activated carboxylic acid or in two steps with isolation of an activated “trapped” carboxylic acid with reaction with an amine.

Two step peptide bond formation


The carboxylate reacts with the coupling reagent yielding a reactive intermediate which can often be isolated or used immediately with an amine to form an amide bond.  A wide variety of reagents have commonly been used to generate the activated carboxylic acid such as an acid halide (chloride, fluoride), azides, anhydrides, or carbodiimides.  Additionally, active esters such as pentafluorophenyl or hydroxysuccinimido esters can be prepared as reactive intermediates.  Reactive intermediates derived from generation of acyl chlorides or azides are highly efficient for amide coupling; however, their harsh formation and high reactivity often limits use with complex substrates or amino acids.  A broadly applicable method for the formation of amide bonds use carbodiimides such as DCC (dicyclohexylcarbodiimide) or DIC (diisopropylcarbodiimide) for activation.  Additives are often required to improve the efficiency of the reactions especially for solid-phase synthesis.


To avoid side reactions involving the substituents on the two coupling components, it is often necessary to carefully select the appropriate peptide-coupling reaction condition.   One common problem with the use of carbodiimides is the racemization of amino acids.   To remedy this, two classes of coupling reagents:  Phosphonium and aminium reagents represent significant improvements over carbodiimide methods.

Common Aminium reagents


Common Phosphonium reagents


Aminium salts are very efficient peptide coupling reagents with quick reaction times and minimal racemization.  With the addition of an additive such as HOBt, racemization can be completely eliminated.  Aminium reagents are used in equal molarity to the carboxylic acid to prevent excess reagent reacting with the free amine of the peptide preventing coupling.  Phosphonium salts react with carboxylate requiring usually 2 equivalent of base.  (such as DIEA).  One key advantage for the use of phosphonium salts over iminium reagents is that phosphonium does not reactive with the free amino group of the amine component.  This allows couplings to occur in equimolar relation between the acid and amine, highly advantageous in situations such as the intramolecular cyclization of linear peptides or examples where excess of valuable amine component is discouraged.

Choosing the correct reaction for your needs:

While amide bond formation is a straightforward reaction, the choice of suitable reagents for an individual coupling of a complex carboxylic acid and amine may be a difficult decision.  A variety of factors can be involved in finding the optimal peptide coupling reaction.  Unanticipated side reactions or rearrangements, low conversions, solubility issues, or incompatibility with additional synthetic steps can all hinder what would appear to be a straightforward amide coupling reaction.  As such, it is often necessary to draw from the large number of available reagents and protocols to find the optimal reaction condition.  Screening a selection of reagents can often find a suitable reaction for any amide coupling.




1.  Brown, Dean G., Bostrom, Jonas, “Analysis of Past and Present Synthetic Methodologies on Medicinal Chemistry:  Where Have All the New Reactions Gone?” J. Med. Chem., 2015, ASAP.

2.  El-Faham, Ayman; Albericio, Fernando, “Peptide Coupling Reagents, More than a Letter Soup” Chem. Rev., 2011, 111, 6557.

2.  Pattabiraman, Vijaya R., Bode, Jeffrey W. “Rethinking Amide Bond Synthesis” Nature, 2011, 480, 471.

Magic methyl in medicinal chemistry

Methyl groups are very common in drug molecules. As reported by Heike Schonherr and Tim Cernak1, more than half of the top-selling drugs contains a CH3. A simple substitution of a C-H with a methyl can increase the potency of a compound by more than 100-fold.

The effect of C-H methylation primarily affects the conformation of the original molecule.  Based on this reported statistical analysis2 the effect of methyl can be equally positive or negative. However a positive effect could be decisive in a drug discovery program.

Effect of ortho substitution3,4.



Effect of ring substitution5


Effect on rotatable bond6


Even if the methyl can be seen as a potential hot spot for metabolism. The addition of the methyl next to a metabolism position can improve metabolic stability.7



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  1. Heike Schonherr and Tim Cernak, Angew. Chem Int. Ed. 2013, 52, 12256-12267
  2. C. S. Leung, S. S. F. Leung, J. Tirado-Rives, W. L. Jorgensen, J. Med. Chem. 2012, 55, 4489 – 4500.
  3. F. Berardi, C. Abate, S. Ferorelli, A. F. de Robertis, M. Leopoldo, N.A. Colabufo, M. Niso, R. Perrone, J. Med. Chem. 2008, 51, 7523 – 7531.
  4. J. Y. Hwang, D. Smithson, F. Zhu, G. Holbrook,M. C. Connelly, M. Kaiser, R. Brun, R. K. Guy, J. Med. Chem. 2013, 56, 2850 – 2860.
  5. P. J. Coleman and coll. , Chem- MedChem 2012, 7, 415 – 424.
  6. G. F. Costello, R. James, J. S. Shaw, A.M. Slater, N. C. J. Stutchbury, J. Med. Chem. 1991, 34, 181 – 189.
  7. R.W. Friesen and coll., Bioorg. Med. Chem. Lett. 1998, 8, 2777 – 2782.



Buchwald palladium precatalysts

Palladium based catalysis is the most used tool to perform the formation of C-C, C-O and C-N. There are many sources of palladium such as PdOAc2, PdCl2 or Pd2dba3. However the related methods do not always allow sufficient conversion.

Palladium precatalysts is an efficient solution to generate in-situ the LnPd(0) needed for the reaction. These precatalysts are generally air and moisture stable.

The first palladacycle precatalyst has been reported by Herman and Beller in 19951. Since then Buchwald laboratories has developed several types of palladium.

The first generation of Buchwald palladium precatalysts are phenethylamine derivatives. In presence of a base the LPd(0) can be generated in-situ.



The second generation of Buchwald palladium precatalysts are 2-aminobiphenyl derivatives. These precatalysts can be activated at room temperature.


The third generation of Buchwald palladium precatalysts are methylsulfonate salt of 2-aminobiphenyl derivatives. These precatalysts are compatible with bulky ligands and show longer stability in solution.


The fourth generation of Buchwald palladium precatalysts are methylsulfonate salt of 2-methylaminobiphenyl derivatives. These precatalysts are compatible with bulky ligands and show longer stability in solution.





1 Herman,W.A.; Beller,M. Angew. Chem. Int. Ed., 1995, 34, 1844-1848.


Why is fluorine so attractive to medicinal chemists?

In medicinal chemistry, fluorine substitution of alkyl or aryl hydrogen is an increasingly popular strategy to optimize lead compounds. Fluorine offers unique properties. It is almost as small as a hydrogen but very electronegative. The C-F bond is highly polarized.

Conformation effect of fluorine

The polarity of the C-F bond influences the conformation of aliphatic systems.


It is generally accepted that fluorine can interact with hydroxyl, amine and amide functions through hydrogen bond interaction and induce specific conformation.


Influence on pKa, permeability and pharmacokinetic properties of fluorine

The electron-withdrawing properties of fluorine can reduce pKa of amines and make them less basic. The similar effect is observed on carboxylic acids and make them more acidic. The change in pKa will influence conformation, potency, permeability, and pharmacokinetic properties.

pKa of fluorinated acids, alcohols or amines

CH3CO2H      4.8       CH2FCO2H    2.6

(CH3)2CHOH 17.1     (CF3)2CHOH  9.3

CH3CH2NH2  10.7      CF3CH2NH2   5.7

Improve metabolic stability

Because of the strength C-F bond, fluorine substitution of a hydrogen is a common way to improve stability. It can be done in both aliphatic and aromatic systems. Fluorine will also increase metabolic stability of electron-rich aromatic ring.


Learn how to add fluorine in your lead compounds here.


Read more
Eric P. Gillis, Kyle J. Eastman, Matthew D. Hill, David J. Donnelly, and Nicholas A. Meanwell, Applications of Fluorine in Medicinal Chemistry, J. Med. Chem., 2015


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Unusual Biotransformation of a Pyrrolotriazine Heterocycle

Biotransformations can be diverse and not limited to simple oxidation or dealkylation. An oncologic agent, The BMS-690514, is an example of unexpected metabolism. This compound undergoes multiple biotransformations, among them are P450 mediated oxidations of its heterocycle pyrrolotriazine group. Two major metabolites A and B are resulting from + O biotransformation.  However if the metabolite A shows a hydroxylation of the heterocycle, the metabolite B seems to undergone a unusual rearrangement. The isolation of that metabolite demonstrated the formation a hydroxypyridotriazine group.

This structure was confirmed using NMR spectrometry. The metabolism study of deuterium and tritium isotope label at the oxidized position showed that the label was retain during the formation of the metabolite A and lost during the formation of the metabolite B. The authors concluded that this metabolite was formed via epoxidation.

Haizheng Hong et al. Chem. Res. Toxicol. 201124, 125-134.

Mitochondrial Liabilities Assay and Metabolism with ICDD

Several recent papers have highlighted the importance of identifying mitochondrial liabilities to completely assess the toxicity potential of a drug (1-3).  Mechanisms by which drugs induce organ toxicity include the production of reactive metabolites (4).  Examples such as high-dose acetaminophen, which produces metabolites toxic to the mitochondria are found in the literature (5-8). 

Metabolites or cocktails of metabolites obtained through the Hepatochem technologies may act on one or several mitochondrial targets to induce mitochondrial impairment.  ROS production or reduced anti-oxidant defenses, perturbation of the bioenergetic balance, induction of permeability transition, depletion of mtDNA or reduced mitochondrial mass are some of the various targets that may induce mitochondrial dysfunction, loss of susceptible cell integrity & ultimately organ malfunctions and/or failure (7,9-12).  Using the MitoSafe line of functional bioassays developed by ICDD will demonstrate whether metabolites of your drugs induce mitochondrial liabilities in live-cell models.  Mitochondria toxicity is most readily expressed clinically by hepatic injury & cardio-toxicity, which can both be flagged through the study of your compounds and their metabolites with the MitoSafe bioassays.

Don’t hesitate to ask questions to our mitochondria

1- Marroquin LD, Hynes J, Dykens JA, Jamieson JD, Will Y. Toxicol Sci. 2007 ;97(2):539-47.

2- Dykens JA, Will Y. Drug Discov Today. 2007 ;12(17-18):777-85.

3- Begriche K, Massart J, Robin MA, Borgne-Sanchez A, Fromenty B.  J Hepatol. 2011 ;54(4):773-94.

4- Liebler DC, Guengerich FP.  Nat Rev Drug Discov. 2005 ;4(5):410-20.

5- Kostrubsky SE, Strom SC, Ellis E, Nelson SD, Mutlib AE. Chem Res Toxicol. 2007 ;20(10):1503-12.

6- Jaeschke H, McGill MR, Williams CD, Ramachandran A.  Life Sci. 2011 25;88(17-18):737-45.

7- Song Y, Shi Y, Yu H, Hu Y, Wang Y, Yang K. Toxicol Lett. 2011 ;202(1):55-60.

8- Chaudhuri L, Sarsour EH, Goswami PC. Environ Int. 2010 ;36(8):924-30.

9- Siu WP, Pun PB, Latchoumycandane C, Boelsterli UA.  Toxicol Appl Pharmacol. 2008 ;227(3):451-61.

10- Bai J, Nakamura H, Ueda S, Kwon YW, Tanaka T, Ban S, Yodoi J. J Biol Chem. 2004 ;279(37):38710-4.

11- Ramachandran A, Lebofsky M, Weinman SA, Jaeschke H.Toxicol Appl Pharmacol. 2011 ;251(3):226-33.

12- Zou W, Roth RA, Younis HS, Burgoon LD, Ganey PE. Toxicology. 2010 ;272(1-3):32-8. 

Metalloporphyrin Reactivity

Metalloporphyrins are powerful catalysts capable of a wide variety of chemical transformations. Simple modifications to the catalyst system allow for tuning a catalyst for relatively mild oxidations or more difficult to oxidize substrates. Recently, Zhdankin and coworkers have demonstrated a co-catalyst system with an iron porphyrin with a mixture of iodobenzene and oxone allowing for the quantitative conversion of anthracene to anthroquine (1). This system has also shown promise for the oxidation of alkanes and alkenes such as tetrahydronaphthalene, dihydroanthrane and styrene in moderate yields.

With tuning of the catalyst and reaction conditions, metalloporphyrins are also capable of mild oxidations such as sulfoxidations even in the presence of reactive C-H or alcohol functional groups. Huang and coworkers have used a manganese porphyrin-hypochlorite system for the selective oxidation of glycosyl sulfides to the sulfoxides with high diasteromeric excesses (2). Very little sulfone formation and no oxidation on the sugar occurred. These two recent examples show both the selectivity and powerful oxidation capabilities of metalloporphyrins.

1. Yoshimura, A.; Neu, H. M.; Nemykin, V. N.; Zhdankin, V. V., Metalloporphyrin/Iodine(III)-Cocatalyzed Oxygenation of Aromatic Hydrocarbons. Advanced Synthesis & Catalysis 2010, 352, (9), 1455-1460.
2. Huang, J. Y.; Li, S. J.; Wang, Y. G., Selective Oxidation of Glycosyl Sulfides to Sulfoxides with Sodium Hypochlorite and Catalyzed by Metalloporphyrins. Journal of Carbohydrate Chemistry 2010, 29, (3), 142-153.

Structure-Activity Relationship of Hepatotoxicity

Drug induced liver injury is a major cause for withdrawing a drug from development or more dramatically from the market. In a recent article, Dr. Dennis J. Pelletier et Al. performed a SAR study of hepatotoxicity. They used the data from literature and built a structure searchable database. The resulting database was analyzed to identify the chemical structures associated with liver toxicity. Data from over 1266 compounds were collected and a SAR of 38 chemical structures was developed. An interesting chemical structure highlighted as a potential liver toxin is the thiophene ring. Metabolic activation of thiophene leads to a reactive intermediate that can undergo Michael type addition with cellular nucleophiles. See figure below.


Interestingly, hepatotoxicity is often due to an activation of the drug resulting from Phase I metabolization. Moreover, this kind of reactive metabolite is present at low levels in the blood stream which makes them difficult to be detected.
Biomimetic technology can allow for the production of such metabolites for biological and toxicology studies which could reduce the drug development attrition due to liver toxicity.
Dennis J. Pelletier et Al.; Chem. Res. Toxicol., 2010, 23, 1215-1222

SMARTCyp: a Wed Based CYP-Mediated Metabolism Prediction Tool

We would like to bring to your attention to a new metabolism tool available online. Lars Olsen et al. have developed a web based platform that predicts potential sites of metabolization. This free tool is the first web service for prediction of CYP-mediated metabolism. Based on a recent publication from Simon E. Ward et al. where they describe the metabolism pathway of a novel clinical AMPA receptor positive modulator, we tested the prediction tool and the result confirmed the potential utility of this application for the prediction of CYP-mediated metabolism.

Patrik Rydberg, David E. Gloriam and Lars Olsen. Bioinformatics 2010, 26, 2988-2989.

Simon E. Ward et al. J. Med. Chem. 2010, 53, 5801-5812

Fluorine and Deuterium to Improve Oral Bioavailability

In a recent article, Dr Angela D. Kerekes et al. described the PK optimization of a potent Aurora inhibitor 1. This compound presents a good PK profile for intravenous delivery but poor oral bioavailability in rats due to rapid metabolism and poor oral absorption. Metabolism studies determine that the compound undergoes N-desethyl and oxidation to generate metabolites 2 and 3.

To improve the PK, the initial strategy was to block N-Alkylation by introduction of fluorine (see compound 4). This modification improved the oral PK in rat but oral PK in monkey was unchanged. In further metabolism studies the failure of the fluorine addition to improve oral PK was attributed to an additional hydroxylation of the arylic position. The introduction of deuterium to that position resulted in a improved oral PK in monkey (see compound 5). This example demontrates that introduction of fluorine and deuterium when possible can be an excellent strategy to improve oral PK.

Angela D. Kerekes et al. J. Med. Chem. 2011 asap