In silico screening as an effective tool in drug discovery

According to statistics published by the World Health Organization (WHO), tuberculosis (TB) is globally one of the leading causes of death from a curable infectious disease. While antibiotics represent a major breakthrough for modern medicine, the spread of multi-drug resistant (MDR) bacterial strains, such as Mycobacterium tuberculosis, have become a major threat to healthcare.

Encouragingly, renewed efforts in antibiotic research have resulted in the identification of new leads, some of which are currently in clinical trials. Even in light of these promising efforts, Dr. Ehmke Pohl of Durham University and collaborators from the Cambridge Crystallographic Data Centre and Institut Pasteur de Lille are emphasizing the need to optimize existing TB treatments as well as develop an efficient means of identifying novel therapeutics.

Structure-based drug discovery is an integral part of most industrial drug discovery programs and as a result, there is an ever-growing number of protein X-ray crystal structures available in databases such as the Protein Data Bank (PDB). Pohl and collaborators outline a robust and versatile strategy for an in silico screening protocol based on compounds in the ZINC database (a free resource of commercially available chemical compounds) and crystal structures in the PDB.

Their current OBC study focuses on the transcriptional regulator EthR which is involved in M. tuberculosis resistance. EthR has been shown to limit the efficacy of ethionamide-based drugs by downregulating the EthA enzyme involved in activation of ethionamide prodrugs. EthR has therefore been validated as a suitable target as its inhibition boosts ethionamide action.

Using tailored chemical and physicochemical descriptors (for example: compound volume) and a detailed knowledge of the EthR binding pocket, approximately 6 million compounds were evaluated for compatibility using KNIME pipeline software. 409 201 diverse compounds were identified for docking studies and surprisingly, only 6 compounds failed to produce feasible binding interactions. After a careful post-docking filter, 284 chemically diverse compounds were obtained and a visual analysis of all binding poses and ligand geometries in combination with computational analysis narrowed the screen down to 85 substrates. These in silico hits were then evaluated for their capability to bind to EthR using thermal protein stability studies which resulted in 20 new potential candidates for lead optimization with reasonable EC50 values.

Given the ever-growing number of high resolution crystal structures in the PDB, in silico screening approaches can be tailored to any well-characterized protein structure and utilized as an efficient tool for identifying new active molecules.

To find out more see:

New active leads for tuberculosis booster drugs by structure-based drug discovery
Natalie J. Tatum, 
DOI:10.1039/C7OB00910K


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at the University of Toronto. Her research is centred on the synthesis of kinetically amphoteric building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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An unusual hydride source for reductive aminations

The reductive amination reaction between amines and carbonyls is a highly useful and versatile means of forming C-N bonds. Given the accessibility of starting materials and its modular nature, reductive aminations have found extensive application not only in organic synthesis but medicinal chemistry and the production of agro- and industrial chemicals.

Developing efficient and economical processes to access valuable materials is a priority in industry. One of the most fundamental ways of doing this is to adhere to the principle of atom economy which moves to minimize waste generated by a chemical reaction at the molecular level. While traditionally, chemists have focused on improving yield or minimizing the number of steps in a reaction sequence, atom economy aims to design reactions in which all atoms involved in a chemical process are present in the desired products.

An international team of researchers have recently published a novel iridium-catalyzed reductive amination using carbon monoxide (CO) as an alternative reductant. This process does not require an external hydrogen source as the hydride is abstracted by the catalyst/carbon monoxide complex from the hemiaminal intermediate, forming an iridium-hydride species. Essentially, the hydride is derived internally (from the amine) as a result of the deoxygenative potential of carbon monoxide. The reaction is also tolerant to a number of functional groups that are incompatible with other commonly employed reducing reagents.

This is a very interesting twist on the reductive amination reaction for which external sources of hydrogen are often required. While it could be called atomic economic from this standpoint, the fact that carbon dioxide is a major by product of the reaction detracts from this claim and could be problematic on an industrial level. Regardless, this work is a significant first step and demonstrates the importance of optimizing the efficiency of well-established protocols in organic synthesis for large scale purposes.

To find out more see:

Reductive amination catalyzed by iridium complexes using carbon monoxide as a reducing agent

DOI:10.1039/C7OB01005B


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at the University of Toronto. Her research is centred on the synthesis of kinetically amphoteric building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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The effect of polymer architecture on the self-assembly and stability of complex coacervation

Complex coacervation refers to a liquid-liquid phase separation that arises from the association of oppositely charged polyelectrolytes in water. It is a widely used laboratory technique and coacervate-based materials have extensive application in the food and cosmetic industries as well as drug delivery and the development of biomedical adhesives.

Under favourable conditions, the coalescence of coacervate droplets leads to a separation of a system into two liquid layers: a polymer-rich coacervate phase in equilibrium with a polymer poor supernatant. Coacervation is entropically driven and occurs through an initial electrostatic attraction between oppositely charged molecules followed by the release of counterions and rearrangement of water molecules. However, our understanding of factors that control self-assembly and stability at the molecular level remains limited.

In the past, many studies have focused on how the chemical nature of a polymer affects coacervation without considering the effect of polymer architecture. In a collaborative study recently published in OBC, Prof. Sarah Perry and Prof. Todd Emerick et al., of the University of Massachusetts Amherst investigate the effect of branching in polypeptide-based comb polymers on the self-assembly and stability of complex coacervates.

In comparison to branched copolymers, the interaction of oppositely charged linear copolymers to form charge-neutral coacervate complexes is understandably straightforward. However, the extent to which a mismatched polymer architecture would alter coalescence is relatively unclear and a question that Perry and Emerick sought to answer.

The self-assembly and stability of complex coacervates resulting from oppositely charged linear polymers, linear and comb polymer and two comb polymers (see Figure) were determined/compared through turbidity measurements, optical microscopy and Monte Carlo simulations. Ultimately, it was observed that the comb structure did not form coacervates as the branched structure prevents cooperative interactions between oppositely charged polymer pairs and releases fewer counterions, leading to a weaker driving force for coacervation.

This study provides insight to the role that polymer architecture plays on complex coacervation and highlights the need to develop a detailed and predictable understanding of molecular level effects of polymer chemistry and architecture in coacervate formation.

To find out more see:

The effect of comb architecture on complex coacervation
Brandon M. Johnston,  10.1039/C7OB01314K


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at the University of Toronto. Her research is centred on the synthesis of kinetically amphoteric building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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Unexpected divergent reactivity in Pt-catalyzed cyclizations of 1,5-bisallenes

As a result of their unique physical and chemical properties, allenes have become key building blocks in modern organic synthesis. The discovery and development of their varied reactivity have been extensively reported on in recent years, however, application to more challenging bisallene systems has been comparatively limited.

In her group’s recent OBC publication, Prof. María Paz Muñoz of the University of East Anglia sought to fill this gap in the bisallene literature. The study discusses the development of an unprecedented Pt-catalyzed cyclization of 1,5-bisallenes in the presence of oxygen nucleophiles to selectively access 6- and 7-membered rings.

After initial screening, it was observed that selectivity was highly sensitive to the reaction conditions and could, therefore, be tuned to yield the desired molecular scaffold. Interestingly, in the presence of nucleophilic alcohols, vinyltetrahydropyridines are formed preferentially while the formation of di- and tetrahydroazepines are favoured when water is used.

Exhaustive mechanistic studies provided insight into this divergent reactivity. It was determined that different mechanisms operate depending on the nucleophile and electronic nature of the bisallene (as a result of its nitrogen tether). It is proposed that, in the presence of nucleophilic alcohols, 6-membered vinyltetrahydropyridines are preferentially formed as a result of a platinum hydride active catalyst—which are known to form from platinum complexes and alcohols. Tetrahydroazepines, on the other hand, are favoured when water is used as the nucleophile, proceeding first through a nucleophilic attack followed by carbocylization to form the 7-membered ring.

Understanding this complex mechanistic behaviour provides important insight into bisallene reactivity and will no doubt enhance the scope of this work’s application in organic and medicinal chemistry.

This communication is part of the OBC themed collection, Mechanistic Aspects of Organic Synthesis. You can read the rest of the collection here.

 

To find out more see:

Nucleophile dependent formation of 6- and 7-membered N-heterocycles by platinum-catalysed cyclisation of 1,5-bisallenes
María Teresa Quirós,César Hurtado-Rodrigo and María Paz Muñoz
DOI:10.1039/C7OB01469D


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at the University of Toronto. Her research is centred on the synthesis of kinetically amphoteric building blocks which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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What are your colleagues reading in Organic & Biomolecular Chemistry?

The articles below are some of the most read Organic & Biomolecular Chemistry articles in April, May and June 2017.

Review Articles:

Design and synthesis of analogues of natural products
Martin E. Maier
DOI: 10.1039/C5OB00169B

Transition-metal catalyzed valorization of lignin: the key to a sustainable carbon-neutral future
Markus D. Kärkäs, Bryan S. Matsuura, Timothy M. Monos, Gabriel Magallanes and Corey R. J. Stephenson
DOI: 10.1039/C5OB02212F

Selective chemical labeling of proteins
Xi Chen and Yao-Wen Wu
DOI: 10.1039/C6OB00126B

Site-selective incorporation and ligation of protein aldehydes
Richard J. Spears and Martin A. Fascione
DOI: 10.1039/C6OB00778C

1,3-Dipolar cycloadditions of azomethine imines
Carmen Nájera, José M. Sansano and Miguel Yus
DOI: 10.1039/C5OB01086A

Organocatalytic synthesis of axially chiral atropisomers
P. Renzi
DOI: 10.1039/C7OB00908A

The application of design of experiments (DoE) reaction optimisation and solvent selection in the development of new synthetic chemistry
Paul M. Murray, Fiona Bellany, Laure Benhamou, Dejan-Krešimir Bučar, Alethea B. Tabor and Tom D. Sheppard
DOI: 10.1039/C5OB01892G

Recent advances in the synthesis and application of fluorescent α-amino acids
Alexander H. Harkiss and Andrew Sutherland
DOI: 10.1039/C6OB01715K

Communications & Papers:

Amidation of unactivated ester derivatives mediated by trifluoroethanol
Christopher G. McPherson, Nicola Caldwell, Craig Jamieson, Iain Simpson and Allan J. B. Watson
DOI: 10.1039/C7OB00593H, Communication

A rapid and efficient one-pot method for the reduction of N-protected α-amino acids to chiral α-amino aldehydes using CDI/DIBAL-H
Jakov Ivkovic, Christian Lembacher-Fadum and Rolf Breinbauer D
OI
: 10.1039/C5OB01838B, Communication

A protocol for amide bond formation with electron deficient amines and sterically hindered substrates
Maria E. Due-Hansen, Sunil K. Pandey, Elisabeth Christiansen, Rikke Andersen, Steffen V. F. Hansen and Trond Ulven
DOI: 10.1039/C5OB02129D, Communication

A NHC-catalyzed 1,3-dipolar cycloaddition reaction of allyl ketones with azides: direct access to 1,4,5-trisubstituted 1,2,3-triazoles
Huijun Yuan, Lili Zhang, Zhantao Liu, Yang Liu, Jian Wang and Wenjun Li
DOI: 10.1039/C7OB00906B, Communication

A novel off–on fluorescent probe for sensitive imaging of mitochondria-specific nitroreductase activity in living tumor cells
Bo Huang, Wen Chen, Yong-Qing Kuang, Wei Liu, Xian-Jun Liu, Li-Juan Tang and Jian-Hui Jiang
DOI: 10.1039/C7OB00781G, Communication

FeCl3 catalysed 7-membered ring formation in a single pot: a new route to indole-fused oxepines/azepines and their cytotoxic activity
K. Shiva Kumar, Meesa Siddi Ramulu, Bandari Rajesham, N. Praveen Kumar, Vani Voora and Rama Krishna Kancha
DOI: 10.1039/C7OB00715A,Paper

Copper-catalyzed oxidative decarboxylative coupling of α-keto acids and sulfoximines
Chaleena Pimpasri, Ladawan Sumunnee and Sirilata Yotphan
DOI: 10.1039/C7OB00776K, Paper

Tf2NH-catalyzed formal [3 + 2] cycloaddition of oxadiazolones with ynamides: a simple access to aminoimidazoles
Yingying Zhao, Yancheng Hu, Xincheng Li and Boshun Wan
DOI: 10.1039/C7OB00701A, Communication

Cyclic dipeptide based cell-penetrating peptidomimetics for effective DNA delivery
Chilakapati Madhu, Chandrashekhar Voshavar, K. Rajasekhar and Thimmaiah Govindaraju
DOI: 10.1039/C7OB00167C, Communication

Synthesis, properties, and crystal structures of π-extended double [6]helicenes: contorted multi-dimensional stacking lattice
Takao Fujikawa, Nobuhiko Mitoma, Atsushi Wakamiya, Akinori Saeki, Yasutomo Segawa and Kenichiro Itami
DOI: 10.1039/C7OB00987A, Paper

Urotensin-II peptidomimetic incorporating a non-reducible 1,5-triazole disulfide bond reveals a pseudo-irreversible covalent binding mechanism to the urotensin G-protein coupled receptor
Salvatore Pacifico, Aidan Kerckhoffs, Andrew J. Fallow, Rachel E. Foreman, Remo Guerrini, John McDonald, David G. Lambert and Andrew G. Jamieson
DOI: 10.1039/C7OB00959C, Paper

Enantioselective total synthesis of (+)-arborescidine C and related tetracyclic indole alkaloids using organocatalysis
Vishal M. Sheth, Bor-Cherng Hong and Gene-Hsiang Lee
DOI: 10.1039/C7OB00473G, Communication

Asymmetric synthesis of CF3-containing tetrahydroquinoline via a thiourea-catalyzed cascade reaction
Yuanyuan Zhu, Boyu Li, Cui Wang, Zhenghao Dong, Xiaoling Zhong, Kairong Wang, Wenjin Yan and Rui Wang
DOI: 10.1039/C7OB01013C, Communication

Palladium-catalyzed Suzuki–Miyaura coupling of amides by carbon–nitrogen cleavage: general strategy for amide N–C bond activation
Guangrong Meng and Michal Szostak
DOI: 10.1039/C6OB00084C, Paper

Ru(II)-Catalyzed annulation of benzamidines and alkynes by C–H/N–H activation: a facile synthesis of 1-aminoisoquinolines
P. P. Kaishap, G. Duarah, D. Chetia and S. Gogoi
DOI: 10.1039/C7OB00389G, Paper

2,2,2-Trifluoroethanol as a solvent to control nucleophilic peptide arylation
Diana Gimenez, Anica Dose, Nicholas L. Robson, Graham Sandford, Steven L. Cobb and Christopher R. Coxon
DOI: 10.1039/C7OB00295E, Communication

Regioselective 6-endodig iodocyclization: an accessible approach for iodo-benzo[a]phenazines
Sonu Kumar, Mohammad Mujahid and Akhilesh K. Verma
DOI: 10.1039/C7OB00671C, Paper

Keep up-to-date with the latest issues of Organic & Biomolecular Chemistry with our E-alerts

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Poster prize winners at the 11th Symposium on Biorelevant Chemistry

Congratulations to the poster prize winners at the Symposium on Biorelevant Chemistry!

Organic & Biomolecular Chemistry are please to present prizes to these winners:

Ryotaro Yamada (Nagoya University, Graduate School of Science, Department of Chemistry)
Title: Probing auxin signaling with synthetic auxin-engineered receptor pair

Kieko Senda (Nagoya University, Graduate School of Science, Department of Chemistry)
Title: Photostable fluorescent nanoparticles encapsulating a NIR phospha-rhodamine dye

Organised by the Chemical Society of Japan, the Symposium on Biorelevant Chemistry took place from the 7th – 9th September 2017.

The winners receiving their prizes from Philippa Hughes (Executive Editor, Royal Society of Chemistry)

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Inspired by nature: dynamic stimuli responsive catalysis based on molecular motors

Catalysis is a fundamental concept in chemistry, allowing chemists to effectively carry out difficult transformations to access valuable materials with precision and control. For the most part, research has focused on the development of new catalysts for optimized performance to achieve high conversion and selectivity. However, special attention is now being paid to engineering catalysts whose activity can be tuned through external stimuli. This concept is ubiquitous in nature and its implementation into artificial systems offers unique opportunities and promising future applications.

A recent OBC publication by Prof. Ben Feringa of the University of Groningen Nijenborgh discusses his group’s success in developing two novel bisthiourea catalysts which display dynamic control over activity and stereoselectivity in the Henry reaction using light and heat as external stimuli.

This catalyst design is based on a molecular motor previously reported by Feringa and inspired by nature where control over function, activity and selectivity can be attained through conformational changes within the catalyst’s active site induced by external stimuli.

In the current publication, upon irradiation of the catalyst in its stable trans state, (R,R)-(P,P)-trans (see Scheme), an unstable cis state is obtained, (R,R)-(M,M)-cis, in which the catalytic groups A and B are brought into proximity to carry out the desired enantioselective transformation. The catalyst can then be converted through heating to a stable cis state, the (R,R)-(M,M)-cis isomer, via a thermal helix inversion. In this conformation, the two active groups A and B remain within reaction proximity, however, as the helicity of the motor core is inverted, a pseudoenantiomeric catalytic environment is produced which results in the formation of the opposite enantiomer.

This is the first example of a tunable bisthiourea catalyst and represents an important advancement in the field of dynamic stimuli responsive catalysis. This new area of research offers great potential for advanced materials and solving long-standing challenges that have thus far been impossible to overcome using conventional methodologies.

To find out more see:
Dynamic control over catalytic function using responsive bisthiourea catalysts
M. Vlatković,  
DOI:10.1039/C7OB01851G


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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Organic & Biomolecular Chemistry partners with Publons

Organic & Biomolecular Chemistry has partnered with Publons (a third-party reviewer recognition service) so you can keep a record of every review you complete.

We really value your reviewing and editorial contributions and want to ensure you get more recognition for them.

How it works
When you submit a review to a participating journal you will be asked if you want to opt in to Publons, you can then instantly start building your verified peer review and editorial record to showcase the full extent of your contributions and influence in your field. Publons tracks your reviews without compromising reviewer anonymity, by default, only the year of the review and the journal title will be shown on reviewer profiles for our journals.

Read more about the partnership on our news pages

For more information about Publons, visit publons.com/benefits/researchers

 

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Poster Prize Winners at the Tri-Institutional Chemical Biology Symposium

From the whole Organic & Biomolecular Chemistry team, we’d like to say congratulations to all the poster prize winners at the Tri-Institutional Chemical Biology Symposium 2017!

We were pleased to present prizes to the following winners:


Rudolph Pisa
(Graduate student with Professor Tarun Kapoor, The Rockefeller University) – Chemical Science poster prize
A rational strategy to design probes for the chemical genetic analysis of AAA+ proteins

Darren Johnson (Graduate student with Professor Daniel Bachovchin, Memorial Sloan Kettering Cancer Centre) – Chemical Society Reviews poster prize
DPP8 and DPP9 are therapeutic targets for acute myeloid leukemia

Michaelyn Lux (Graduate student with Professor Derek Tan, Memorial Sloan Kettering Cancer Centre) – Organic & Biomolecular Chemistry poster prize
Diastereoselective palladium-catalyzed cascade to form pyranobenzofurans and furobenzofurans

Dr Nathan Westcott (Postdoc with Professor Howard Hang, The Rockefeller University) – Organic & Biomolecular Chemistry poster prize
Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress

 

You can read some related papers publishing in Organic & Biomolecular Chemistry below:

A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site
James C. Burnett, Chaemin Lim, Brian D. Peyser, Lalith P. Samankumara, Marina Kovaliov, Raffaele Colombo, Stacie L. Bulfer, Matthew G. LaPorte, Ann R. Hermone, Connor F. McGrath, Michelle R. Arkin, Rick Gussio, Donna M. Huryn and Peter Wipf
From themed collection 2017 Hot Articles in Organic and Biomolecular Chemistry

Structure-based design of 3-carboxy-substituted 1,2,3,4-tetrahydroquinolines as inhibitors of myeloid cell leukemia-1 (Mcl-1)
L. Chen, P. T. Wilder, B. Drennen, J. Tran, B. M. Roth, K. Chesko, P. Shapiro and S. Fletcher
From themed collection New Talent

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Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials

Molecular self-assembly has become one of the most prominent fields of nanotechnology in recent years. Inspired by nature, many scientists around the world are attempting to utilize it as a tool to design novel nanostructures with desired biomedical properties.

To achieve this goal, it is necessary to understand how self-assembly works and how molecular forces and other conditions drive this self-assembly and define the structure of a specific supramolecular complex.

In a recent Organic & Biomolecular Chemistry publication, Professor Charlotte J. C. Edwards-Gayle and Professor Ian W. Hamley from the University of Reading, UK, have reviewed some of the most prominent self-assembled peptide amphiphiles and their potential applications. These include tissue scaffolds, antimicrobial peptides and drug transporters.

One of the distinct features of self-assembling amphiphiles, which makes them attractive candidates for many applications, is their diversity to form various structures such as micelles, vesicles, nanotubes, fibrils and sheets (Fig.1). The self-assembly of PAs can also be tuned by several factors including amino acid sequence, peptide length, temperature, pH, and concentration.

 

These features make them perfect, novel tools to create biomaterials which can be responsive to different environmental cues. However, the review points out that the key question of whether there is a relationship between bioactivity and self-assembly of peptide amphiphiles has still remained unanswered, despite the advancement in the field.

Extending the success in designing various structures, together with distinct applications, have made peptide amphiphile self-assembly a vibrant field in which researchers will continue to develop functional constructs with novel applications.

To find out more please see:

Self-assembly of bioactive peptides, peptide conjugates, and peptide mimetic materials
Charlotte J. C. Edwards-Gayle and Ian W. Hamley
DOI: 10.1039/C7OB01092C


Zahra Bahrami Dizicheh is a PhD candidate in molecular biology with Dr. Giovanna Ghirlanda at Arizona State University. She does research on photo-electrochemical hydrogen production with designing and developing interconnection between conductive materials and redox proteins to develop dye-sensitized photo-electrochemical cells.

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