Derivatization Design of Synthetically Accessible Space for Optimization: In Silico Synthesis vs Deep Generative Design.

Molecular design is of utmost importance in lead optimization programs ultimately determining the fate of the project and the speed to reach preclinical stage. Newly designed lead analogues or new chemotypes must successfully address the challenges in the multidimensional optimization process throughout several optimization cycles. The speed, quality, and creativity of the designs can have a major impact on the cycle time, the number of required cycles, and the number of compounds needed to be synthesized and evaluated that in combination affect the overall timeline and cost of the lead optimization phase. Recently, a new concept, generative design with deep learning, has become popular for de novo design of project relevant analogue sets. We have developed a de novo design technology called "derivatization design" that applies artificial-intelligence-assisted forward in silico synthesis for the generation of near neighbor lead analogues as well as scaffold variations. The several attractive features of the methodology include synthetic feasibility, reagent availability and cost data associated with each new molecule; thus, detailed synthetic assessment is automatically generated during the design. As a result, these practically important data types can become an early part of the ranking and selection process for cycle time reduction. The power of derivatization design is demonstrated in a simple design study of DDR1 inhibitors and comparison of the produced molecules to a recently published data set obtained with deep generative design.

Monitoring innate immune cell dynamics in the glioma microenvironment by magnetic resonance imaging and multiphoton microscopy (MR-MPM).

Rationale: Glioblastoma is the most frequent, primary brain tumor that is characterized by a highly immunosuppressive tumor microenvironment (TME). The TME plays a key role for tumor biology and the effectiveness of immunotherapies. Composition of the TME correlates with overall survival and governs therapy response. Non invasive assessment of the TME has been notoriously difficult. Methods: We have designed an in vivo imaging approach to non invasively visualize innate immune cell dynamics in the TME in a mouse glioma model by correlated MRI and multiphoton microscopy (MR-MPM) using a bimodal, fluorescently labeled iron oxide nanoparticle (NP). The introduction of Teflon cranial windows instead of conventional Titanium rings dramatically reduced susceptibility artifacts on MRI and allowed longitudinal MR-MPM imaging for innate immune cell tracking in the same animal. Results: We visualized tumor associated macrophage and microglia (TAM) dynamics in the TME and dissect the single steps of NP uptake by blood-born monocytes that give rise to tumor-associated macrophages. Next to peripheral NP-loading, we identified a second route of direct nanoparticle uptake via the disrupted blood-brain barrier to directly label tissue resident TAMs. Conclusion: Our approach allows innate immune cell tracking by MRI and multiphoton microscopy in the same animal to longitudinally investigate innate immune cell dynamics in the TME.

Hit-to-Lead Optimization and Discovery of 5-((5-([1,1'-Biphenyl]-4-yl)-6-chloro-1H-benzo[d]imidazol-2-yl)oxy)-2-methylbenzoic Acid (MK-3903): A Novel Class of Benzimidazole-Based Activators of AMP-Activated Protein Kinase.

AMP-activated protein kinase (AMPK) plays an essential role as a cellular energy sensor and master regulator of metabolism in eukaryotes. Dysregulated lipid and carbohydrate metabolism resulting from insulin resistance leads to hyperglycemia, the hallmark of type 2 diabetes mellitus (T2DM). While pharmacological activation of AMPK is anticipated to improve these parameters, the discovery of selective, direct activators has proven challenging. We now describe a hit-to-lead effort resulting in the discovery of a potent and selective class of benzimidazole-based direct AMPK activators, exemplified by 5-((5-([1,1'-biphenyl]-4-yl)-6-chloro-1H-benzo[d]imidazol-2-yl)oxy)-2-methylbenzoic acid, 42 (MK-3903). Compound 42 exhibited robust target engagement in mouse liver following oral dosing, leading to improved lipid metabolism and insulin sensitization in mice.

YAP/TAZ Orchestrate VEGF Signaling during Developmental Angiogenesis.

Vascular endothelial growth factor (VEGF) is a major driver of blood vessel formation. However, the signal transduction pathways culminating in the biological consequences of VEGF signaling are only partially understood. Here, we show that the Hippo pathway effectors YAP and TAZ work as crucial signal transducers to mediate VEGF-VEGFR2 signaling during angiogenesis. We demonstrate that YAP/TAZ are essential for vascular development as endothelium-specific deletion of YAP/TAZ leads to impaired vascularization and embryonic lethality. Mechanistically, we show that VEGF activates YAP/TAZ via its effects on actin cytoskeleton and that activated YAP/TAZ induce a transcriptional program to further control cytoskeleton dynamics and thus establish a feedforward loop that ensures a proper angiogenic response. Lack of YAP/TAZ also results in altered cellular distribution of VEGFR2 due to trafficking defects from the Golgi apparatus to the plasma membrane. Altogether, our study identifies YAP/TAZ as central mediators of VEGF signaling and therefore as important regulators of angiogenesis.

Prognostic value of interim and restaging PET/CT in Hodgkin lymphoma. Results of the CHEAP (Chemotherapy Effectiveness Assessment by PET/CT) study - long term observation.

Very few studies have determined the prognostic value of interim and restaging PET/CT in patients with Hodgkin lymphoma using current standard of care therapy outside clinical trials. We analyzed the effect of the results of interim and restaging PET/CT on the survival (overall- and relapse-free) in patients who received standard first-line treatment based on the stage of disease and risk factors. We investigated the differences between the relapse and non-relapse groups based on the clinical pathological characteristics of patients who had positive interim PET/CT results.Between January 1, 2007 and December 31, 2011, the staging, interim and restaging PET/CT scans of patients with Hodgkin lymphoma were analyzed. The Deauville criteria were used for the evaluation of interim PET/CT scans. One hundred and thirteen Hodgkin lymphoma patients underwent staging, interim and restaging PET/CT scans. None of the therapy was modified based on the interim PET/CT results. The median follow-up time was 43.5 months. A total of 62 early stage patients and 51 advanced stage patients were identified. The five-year overall survival rates were 93.4% in the interim PET negative group and 58% in the interim PET positive group (p<0.001). The five-year relapse-free survival rates for the negative and positive groups were 92.7% and 40.8%, respectively (p<0.001). The negative predictive value was 100% in the early stage group and 82.35% in the advanced stage group. By comparison, the positive predictive values were 53.8% and 58.8%, respectively, in these two groups. In the interim PET positive group, patients over 40 years of age had a significantly higher probability of relapse (p=0.057).The routine clinical use of interim PET/CT is highly recommended based on our investigation. However, patients with positive interim PET/CT results required frequent additional evaluations.

Gaseous reference standards of formaldehyde from trioxane.

We have developed a dynamic reference standard of gaseous formaldehyde based on diffusion of the sublimate of trioxane and thermal conversion to formaldehyde in the gas phase. We have also produced a gravimetric standard for formaldehyde in a nitrogen matrix, also by thermal conversion of the sublimate of trioxane. Analysis of the gravimetric standard with respect to the dynamic standard has confirmed the comparability of the static and dynamic gravimetric values.

Comparison of transpulmonary thermodilution, transthoracic echocardiography and conventional hemodynamic monitoring in neonates and infants after open heart surgery: a preliminary study.

BACKGROUND: Transpulmonary thermodilution (TPTD) is an increasingly popular method used to monitor the complex hemodynamic changes in critically ill children. The purpose of our study was to examine the relationship between transthoracic echocardiographic (TTE) parameters and global hemodynamic variables derived from TPTD and those derived from conventional measurements in infants and neonates undergoing corrective cardiac surgery. METHODS: After approval from the Ethics Committee of Gottsegen György Hungarian Institute of Cardiology and individual parental consent were obtained, patients were prospectively enrolled. In parallel with continuous postoperative conventional monitoring, TPTD was measured four times daily, and TTE was performed once per day. Conventional hemodynamic, TPTD and TTE parameters were compared with weighted linear regression statistics and a Pearson correlation. RESULTS: One hundred forty-five TPTD measurements and 35 TTE examinations of thirteen enrolled patients were analyzed. Global end-diastolic volume index (GEDVI) was correlated with the fractional shortening (SF, r=0.67, P=0.001) measured by TTE. Among the preload parameters, the percentage change of GEDVI between two consecutive time points showed a pertinent correlation with changes of cardiac index (r=0.67, P=0.001) and changes of stroke volume index (r=0.57, P=0.008). Percentage changes in SF demonstrated a strong negative correlation with changes of left ventricular end-systolic diameter (r=-0.86, P<0.001). There was no significant relationship between alterations in arterial or central venous pressure values with TTE or TPTD parameters. CONCLUSION: Both TPTD and TTE may be used in the estimating volumetric preload parameters. The time course of TPTD-derived parameters may have clinical relevance in pediatric critical care practice.

Label-free high-throughput screening via mass spectrometry: a single cystathionine quantitative method for multiple applications.

Label-free mass spectrometric (MS) technologies are particularly useful for enzyme assay design for drug discovery screens. MS permits the selective detection of enzyme substrates or products in a wide range of biological matrices without need for derivatization, labeling, or capture technologies. As part of a cardiovascular drug discovery effort aimed at finding modulators of cystathionine beta-synthase (CBS), we used the RapidFire((R)) label-free high-throughput MS (HTMS) technology to develop a high-throughput screening (HTS) assay for CBS activity. The in vitro assay used HTMS to quantify the unlabeled product of the CBS reaction, cystathionine. Cystathionine HTMS analyses were carried out with a throughput of 7 s per sample and quantitation over a linear range of 80-10,000 nM. A compound library of 25,559 samples (or 80 384-well plates) was screened as singlets using the HTMS assay in a period of 8 days. With a hit rate of 0.32%, the actives showed a 90% confirmation rate. The in vitro assay was applied to secondary screens in more complex matrices with no additional analytical development. Our results show that the HTMS method was useful for screening samples containing serum, for cell-based assays, and for liver explants. The novel extension of the in vitro analytical method, without modification, to secondary assays resulted in a significant and advantageous economy of development time for the drug discovery project.

The influence of lead discovery strategies on the properties of drug candidates.

Despite the widespread acceptance of guidelines related to desirable physicochemical properties of potential small-molecule drugs, key properties - such as lipophilicity - of recently developed clinical candidates and advanced lead compounds have been shown to differ significantly from those of historical leads and drugs. By analysing the physicochemical properties of a large database of hits and corresponding leads identified in the past decade, we show that this undesirable phenomenon can be traced back to the nature of high-throughput screening hits and hit-to-lead optimization practices. Conceptual and organizational adjustments may be required to enable a smooth lead-evolution process that reduces the chance of high compound-related attrition in clinical trials.

On sampling of fragment space.

Fragment-based lead discovery has over the years matured into an attractive alternative to high-throughput screening (HTS) for lead generation. Several techniques for screening libraries of typically 10(3)-10(4) fragments have been reported. In this work, the practical success rates that can be expected from the screening of fragment-like libraries was investigated via interrogating medicinal chemistry databases for several programs with virtual libraries created from commercially available reagents or with libraries of commercially available fragments. The results suggest that hits more potent than typically discovered in today's fragment-based screens can consistently be identified from realistically accessible compound sets under screening conditions similar to commonly used HTS protocols.

Hit discovery and hit-to-lead approaches.

Hit discovery technologies range from traditional high-throughput screening to affinity selection of large libraries, fragment-based techniques and computer-aided de novo design, many of which have been extensively reviewed. Development of quality leads using hit confirmation and hit-to-lead approaches present their own challenges, depending on the hit discovery method used to identify the initial hits. In this paper, we summarize common industry practices adopted to tackle hit-to-lead challenges and review how the advantages and drawbacks of different hit discovery techniques could affect the various issues hit-to-lead groups face.

Improving success rates for lead generation using affinity binding technologies.

Affinity technologies have been applied at several stages of the drug discovery process, ranging from target identification and purification to the identification of preclinical candidates. The detection of ligand-macromolecule interactions in lead discovery is the best studied and most powerful of these techniques. Although affinity methods have been in widespread use for about a decade, only recently have many reports emerged on their utility. Primary affinity screens of large libraries of small molecules or fragments have begun to produce results for challenging targets. Furthermore, in secondary assays affinity methods are opening new avenues to tackle important medicinal chemistry tasks.

Versatile solid-phase synthesis of trisubstituted 1H-pyrido[2,3-d]pyrimidin-4-ones and related heterocycles.

A solid-phase synthesis of trisubstituted 1H-pyrido[2,3-d]pyrimidin-4-ones has been developed. The synthesis utilizes solid-phase bound N-2,6-dichloronicotinoyl-1H-benzotriazole-1-carboximidamides as key intermediates. Sequential substitution of benzotriazole and the two chlorines furnishes the title compounds with regioselectivity and high purity. Application of the method to various disubstituted analogues is also demonstrated.

Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases.

A small molecule nonpeptide inhibitor of beta-secretase has been developed, and its binding has been defined through crystallographic determination of the enzyme-inhibitor complex. The molecule is shown to bind to the catalytic aspartate residues in an unprecedented manner in the field of aspartyl protease inhibition. Additionally, the complex reveals a heretofore unknown S(3) subpocket that is created by the inhibitor. This structure has served an important role in the design of newer beta-secretase inhibitors.

Synthesis, molecular modeling, and evaluation of nonphenolic indole analogs of mycophenolic acid.

Based on the promising activity of an indole-3-carboxamide derivative, a nonphenolic analog of mycophenolic acid (MPA), we report herein the synthesis of a compound containing two important features for the activity of MPA, the ring methoxy and methyl. The synthesis was accomplished using two strategies; a method dependent on stepwise building of the hexenoate side chain followed by the indolecarboxamide ring system, and a convergent route that depended on 1,3-sigmatropic rearrangement as a key step. Docking experiments on both Chinese Hamster and Human Type-II inosine monophosphate dehydrogenase (IMPDH) showed that this compound has potential binding interactions with the NAD site. The analogs showed no activity against MCF7-S, MCF7-R, or IGR-OV1 cancer cells.

Combinatorial synthesis of substituted biaryls and heterocyclic arylamines.

In this paper, we report very general conditions that enable palladium-mediated coupling reactions on the solid support. A wide variety of biaryls and arylamines (including pyrimidines) have been synthesized using this protocol. The chemistry facilitates a combinatorial approach to the production of large numbers of medicinally relevant heterocyclic structures.

A reagent-based strategy for the design of large combinatorial libraries: a preliminary experimental validation.

Combinatorial library design can be carried out at either the reagent or the product level. Various reports in the literature have come to conflicting conclusions in favor of one over the other. In this paper a reagent-based screening library design strategy is presented. The method relies on analysis of scaffolds and building blocks separately to define the overall diversity in a compound file. The primary diversity selection by properties relevant for molecular recognition and by redundancy is followed by the application of filters for molecular properties known to be relevant for drug-likeness. Filter properties are rapidly estimated at the product level using a fragmental estimation approach. Initial experimental data suggest that high diversity in vast screening libraries can be achieved by carefully applied reagent level analysis. A potential role of diverse screening libraries in chemical genomics (pharmacological knockouts) is also discussed.

New developments in chemical library synthesis. Norbornenyl tags for use in phase-switching, sequestration, capture-release and soluble support applications.

A new, general chemical library purification platform is reviewed. This platform makes broad use of (oxa)norbornenyl-tagged reactants, reagents, catalysts, sequestration-enabling reagents and scavengers, in combination with Grubbs catalyst-mediated ring-opening metathesis polymerization (ROMP) reactions as an in situ polymerization purification technique. Extensions of this platform involve the use of preformed ROMP supports in synthesis, and polystyrene-supported Grubbs catalysts, which perform in a boomerang fashion.

Recent advances in chemical library synthesis methodology.

The first part of this review highlights recent advances in polymer-supported reagents, catalysts, reactants and sequestrants. Particular attention is given to recent advances in polymer-supported oxidants, transition metal catalysts and polymer-supported reactants, including acyl groups, guanidinyl groups, alkyl groups and various classes of nucleophiles. This second part of the review highlights recent advances made in the areas of chemical tagging and phase-trafficking techniques, all of which have enabled further advances in the methodology of solution-phase chemical library synthesis.

Solid-phase synthesis of 3-alkylamino-1,2,4-triazoles.

[reaction: see text] A solid-phase synthesis of trisubstituted 3-alkylamino-1,2,4-triazoles has been developed. The synthesis utilizes immobilized N-acyl-1H-benzotriazole-1-carboximidamides as key intermediates. Cyclization with hydrazines under mild conditions furnishes the title compounds with regioselectivity and high purity.