Robust Prediction of Relative Binding Energies for Protein-Protein Complex Mutations Using Free Energy Perturbation Calculations.

Computational free energy-based methods have the potential to significantly improve throughput and decrease costs of protein design efforts. Such methods must reach a high level of reliability, accuracy, and automation to be effectively deployed in practical industrial settings in a way that impacts protein design projects. Here, we present a benchmark study for the calculation of relative changes in protein-protein binding affinity for single point mutations across a variety of systems from the literature, using free energy perturbation (FEP+) calculations.

Urban nitrogen budgets: Evaluating and comparing the path of nitrogen through cities for improved management.

Reactive nitrogen (Nr) released to the environment is a cause of multiple environmental threats. While Nr flows are often only analyzed in an agricultural context, consumption and emission takes place in the urban environment, and opportunities for Nr recycling and effective policy implementation for mitigation often appear in cities. Since little information is available on the bigger picture of Nr flows through the urban environment, these opportunities often remain unexploited.

The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Hit Generation.

Hit generation is a crucial step in drug discovery that will determine the speed and chance of success of identifying drug candidates. Many strategies are now available to identify chemical starting points, or hits, and each biological target warrants a tailored approach. In this set of best practices, we detail the essential approaches for target centric hit generation and the opportunities and challenges they come with.

The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Phenotypic Drug Discovery.

Phenotypic drug discovery has a long track record of delivering innovative drugs and has received renewed attention in the last few years. The promise of this approach, however, comes with several challenges that should be addressed to avoid wasting time and resources on drugs with undesired modes of action or, worse, false-positive hits. In this set of best practices, we go over the essential steps of phenotypic drug discovery and provide guidance on how to increase the chance of success in identifying validated and relevant chemical starting points for optimization: selecting the right assay, selecting the right compound screening library and developing appropriate hit validation assays.

A protein tertiary structure mimetic modulator of the Hippo signalling pathway.

Transcription factors are key protein effectors in the regulation of gene transcription, and in many cases their activity is regulated via a complex network of protein-protein interactions (PPI). The chemical modulation of transcription factor activity is a long-standing goal in drug discovery but hampered by the difficulties associated with the targeting of PPIs, in particular when extended and flat protein interfaces are involved. Peptidomimetics have been applied to inhibit PPIs, however with variable success, as for certain interfaces the mimicry of a single secondary structure element is insufficient to obtain high binding affinities.

Discovery of Covalent Inhibitors Targeting the Transcriptional Enhanced Associate Domain Central Pocket.

Transcriptional enhanced associate domain (TEAD) transcription factors together with coactivators and corepressors modulate the expression of genes that regulate fundamental processes, such as organogenesis and cell growth, and elevated TEAD activity is associated with tumorigenesis. Hence, novel modulators of TEAD and methods for their identification are in high demand. We describe the development of a new "thiol conjugation assay" for identification of novel small molecules that bind to the TEAD central pocket.

The European Federation for Medicinal Chemistry (EFMC) Best Practice Initiative: Validating Chemical Probes.

As part of an initiative aimed to share best practices in Medicinal Chemistry, the European Federation for Medicinal Chemistry (EFMC) is preparing a series of webinars and slide sets focused on the early phase of drug discovery. This educational material is freely accessible through the EFMC. The main target audiences are students or early career scientists and we also believe it will be valuable for experienced practitioners.

TEAD-YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics.

DNA-encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or "hot spot", regions of protein-protein interactions. A DNA-encoded combinatorial peptoid library was designed based on the Ugi four-component reaction by employing tryptophan-mimetic indole side chains to probe the surface of target proteins.

Macrocyclic Modalities Combining Peptide Epitopes and Natural Product Fragments.

"Hot loop" protein segments have variable structure and conformation and contribute crucially to protein-protein interactions. We describe a new hot loop mimicking modality, termed PepNats, in which natural product (NP)-inspired structures are incorporated as conformation-determining and -restricting structural elements into macrocyclic hot loop-derived peptides. Macrocyclic PepNats representing hot loops of inducible nitric oxide synthase (iNOS) and human agouti-related protein (AGRP) were synthesized on solid support employing macrocyclization by imine formation and subsequent stereoselective 1,3-dipolar cycloaddition as key steps.

Identification of Quinolinols as Activators of TEAD-Dependent Transcription.

The transcriptional co-regulators YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif) are the vertebrate downstream effectors of the Hippo signaling pathway that controls various physiological and pathological processes. YAP and TAZ pair with the TEAD (TEA domain) family of transcription factors to initiate transcription. We previously identified a tractable pocket in TEADs, which has been physiologically shown to bind palmitate.

New Modalities for Challenging Targets in Drug Discovery.

Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities".

A cyclic carbo-isosteric penta-depsipeptide: cyclo(Phe(1)-d-Ala(2)-Gly(3)-Phe(4)-APO(5)).

The title compound, cyclo(Phe(1)-d-Ala(2)-Gly(3)-Phe(4)-APO(5)), C26H32N4O5, is the minor diastereoisomer of a cyclic penta-peptidomimetic analogue containing a novel 2-amino-propyl lactone (APO) motif, which displays the same number of atoms as the native amino acid glycine and has a methyl group in place of the carbonyl O atom. The crystal structure presented here allows the analysis of the secondary structure of this unprecedented cyclic carbo-isosteric depsipeptide. The conformation of the central ring is stabilized by an intra-molecular N-H⋯O hydrogen bond between the carbonyl O atom of the first residue (Phe(1)) and the amide group H atom of the fourth residue (Phe(4)).

Cyclic carbo-isosteric depsipeptides and peptides as a novel class of peptidomimetics.

A novel and highly efficient cyclization method has been developed to access a new class of cyclic carbo-isosteric depsipeptides and carbo-isosteric peptides. Our strategy requires easily accessible C-terminal methyl ketone ester or amide functionalized linear precursors as starting materials. The well-known reductive amination has then been used to afford cyclic tetra- to octa-pseudopeptides via a selective intramolecular formation of a glycine peptidomimetic unit under moderate dilution.

Synthesis of a functionalized 7,6-bicyclic spiroimine ring fragment of the spirolides.

The asymmetric synthesis of a functionalized 7,6-spiroimine related to the spirolides is described. Intermolecular Diels-Alder cycloaddition of a chiral trisubstituted dienophile and Danishefsky's diene enabled simultaneous installation of the C7 and C29 stereocenters. Further transformations and late-stage aza-Wittig cyclization afforded the spiroimine in good yield.

(1R,6R,13R,18R)-(Z,Z)-1,18-Bis[(4R)-2,2-dimethyl-1,3-dioxolan-4-yl]-3,16-dimethyl-ene-8,20-diaza-dispiro-[5.6.5.6]tetra-cosa-7,19-diene.

The crystal structure of the title compound, C(34)H(54)N(2)O(4), has been solved in order to prove the relative and absolute chirality of the newly-formed stereocentres which were established using an asymmetric Diels-Alder reaction at an earlier stage in the synthesis. This unprecedented stable dialdimine contains a 14-membered ring and was obtained as the minor diastereoisomer in the Diels-Alder reaction. The absolute stereochemistry of the stereocentres of the acetal functionality was known to be R based on the use of a chiral (R)-tris-ubstituted dienophile derived from enanti-opure (S)-glyceraldehyde.

Synthesis and reactivity of beta-methoxymethyl enecarbamates.

Beta-methoxymethyl enecarbamates (e.g., 1) have been prepared in a single step from alpha-methoxy carbamates.

Synthesis of enantiopure bicyclic alpha,alpha-disubstituted spirolactams via asymmetric Birch reductive alkylation.

The synthesis of enantiopure bicyclic alpha,alpha-disubstituted spirolactams is described using a diastereoselective Birch reductive alkylation as the key step. Hydrogenation of the resultant alkylated cyclohexadienes followed by intramolecular cyclization provides access to enantiopure 8-azaspiro[5.6]dodecan-7-ones.

(1R,6R)-1-Methyl-8-aza-spiro-[5.6]dodecan-7-one.

The crystal structure of the title compound, C(12)H(21)NO, has been investigated to establish the absolute stereochemistry at position 1. The absolute stereochemistry at the quaternary centre at position 6 is established to be R using an asymmetric Birch reductive alkyl-ation reaction for which the stereochemical outcome is known. The crystal structure indicates the presence of two conformers of the bicyclic (1R,6R)-spiro-lactam ring system that differ in the conformation adopted by the six-membered ring.

Interleukin-6 (IL-6) and/or soluble IL-6 receptor down-regulation of human type II collagen gene expression in articular chondrocytes requires a decrease of Sp1.Sp3 ratio and of the binding activity of both factors to the COL2A1 promoter.

Type II collagen is composed of alpha1(II) chains encoded by the COL2A1 gene. Alteration of this cartilage marker is a common feature of osteoarthritis. Interleukin-6 (IL-6) is a pro-inflammatory cytokine that needs a soluble form of receptor called sIL-6R to exert its effects in some cellular models.

[Ultrasound-guided vacuum-assisted biopsy: review of 382 cases].

Purpose: To evaluate the use of US-guided vacuum biopsy for diagnosis and treatment of probably benign breast masses.

Materials And Method: Retrospective review of 382 US guided vacuum biopsies over a 44 months period (september 2001 to may 2005) with the 11-g handheld mammotome. A total of 308 benign tumors, 59 borderline lesions and 15 carcinomas were diagnosed.

[Underestimation of breast carcinoma with 11-gauge stereotactically guided directional vacuum-assisted biopsy].

Purpose: To assess the reliability of vacuum-assisted biopsy in diagnosing and managing atypical ductal hyperplasia and ductal carcinoma in situ of the breast.

Materials And Method: Retrospective review of 2130 stereotactic large-core biopsies in 1638 patients over a 40 month period (January 2000 to May 2003) using the mammotome 11-gauge and a dedicated Fischer table. A total of 135 cases of atypical ductal hyperplasia and 322 cases of ductal carcinoma in situ were diagnosed.