Leveraging a "Catch-Release" Logic Gate Process for the Synthesis and Nonchromatographic Purification of Thioether- or Amine-Bridged Macrocyclic Peptides.

Macrocyclic peptides containing N-alkylated amino acids have emerged as a promising therapeutic modality, capable of modulating protein-protein interactions and an intracellular delivery of hydrophilic payloads. While multichannel automated solid-phase peptide synthesis (SPPS) is a practical approach for peptide synthesis, the requirement for slow and inefficient chromatographic purification of the product peptides is a significant limitation to exploring these novel compounds. Herein, we invent a "catch-release" strategy for the nonchromatographic purification of macrocyclic peptides. A traceless catch process is enabled by the invention of a dual-functionalized N-terminal acetate analogue, which serves as a handle for capture onto a purification resin and as a leaving group for macrocyclization. Displacement by a C-terminal nucleophilic side chain thus releases the desired macrocycle from the purification resin. By design, this catch/release process is a logic test for the presence of the key components required for cyclization, thus removing impurities which lack the required functionality, such as common classes of peptide impurities, including hydrolysis fragments and truncated sequences. The method was shown to be highly effective with three libraries of macrocyclic peptides, containing macrocycles of 5-20 amino acids, with either thioether- or amine-based macrocyclic linkages; in this latter class, the reported method represents an enabling technology. In all cases, the catch-release protocol afforded significant enrichment of the target peptides purity, in many cases completely obviating the need for chromatography. Importantly, we have adapted this process for automation on a standard multichannel peptide synthesizer, achieving an efficient and completely integrated synthesis and purification platform for the preparation of these important molecules.

Asymmetric Hydrogenation of Indazole-Containing Enamides Relevant to the Synthesis of Zavegepant Using Neutral and Cationic Cobalt Precatalysts.

The cobalt-catalyzed asymmetric hydrogenation of indazole-containing enamides relevant to the synthesis of the calcitonin gene-related peptide (CGRP) receptor antagonist, zavegepant (1), approved for the treatment of migraines, is described. Both neutral bis(phosphine)cobalt(II) and cationic bis(phosphine)cobalt(I) complexes served as efficient precatalysts for the enamide hydrogenation reactions, providing excellent yield and enantioselectivities (up to >99.9%) for a range of related substrates, though key reactivity differences were observed. Hydrogenation of indazole-containing enamide, methyl (Z)-2-acetamido-3-(7-methyl-1H-indazol-5-yl)acrylate, was performed on a 20 g scale.

The discovery of UK-369003, a novel PDE5 inhibitor with the potential for oral bioavailability and dose-proportional pharmacokinetics.

This paper describes our recent efforts to design and synthesise potent and selective PDE5 inhibitors and the use of in vitro predictors of clearance, absorption and permeability to maximise the potential for dose-proportional pharmacokinetics and good oral bioavailability in man. Optimisation of the preclinical profile resulted in the identification of UK-369003 (19a) and its nomination as a clinical candidate. The clinical pharmacokinetic and safety profile has enabled us to progress the compound to test its efficacy in patients with lower urinary tract symptoms (LUTS) associated with benign prostatic hyperplasia (BPH) and a paper describing its efficacy has recently been published.

Metal-Micelle Cooperativity: Phosphine Ligand-Free Ultrasmall Palladium(II) Nanoparticles for Oxidative Mizoroki-Heck-type Couplings in Water at Room Temperature.

The amphiphile PS-750-M generates stable, phosphine ligand-free, and catalytically active ultrasmall Pd(II) nanoparticles (NPs) from Pd(OAc)2, preventing their precipitation, polymerization, and oxidation state changes. PS-750-M directly interacts with Pd(II) NP surfaces, as confirmed by high-resolution mass spectrometry and IR spectroscopy, resulting in their high stability. The Pd cations in NPs are most likely held together by hydroxides and acetate ions. The NPs were characterized by HRTEM, revealing their morphology and particle size distribution, and by HRMS and IR, providing evidence for NP-amphiphile interaction. The NP catalytic activity was examined in the context of oxidative Mizoroki-Heck-type couplings in water at room temperature. Hot filtration, hot extraction, and three-phase tests indicate heterogeneous catalysis occurring at the micellar interface rather than homogeneous catalysis occurring in the solution. NMR studies indicate that the catalytic activity stems from metal cation-π interactions of the styrene along with transmetalation by the arylboronic acid, followed by insertion and ß-H elimination to furnish the coupled product along with the reoxidation of Pd by benzoquinone to complete the catalytic cycle. This method is very mild and sustainable, both in terms of NP synthesis and subsequent catalysis, and shows broad substrate scope while circumventing the need for organic solvents for this important class of couplings.

Shielding Effect of Nanomicelles: Stable and Catalytically Active Oxidizable Pd(0) Nanoparticle Catalyst Compatible for Cross-Couplings of Water-Sensitive Acid Chlorides in Water.

Under the shielding effect of nanomicelles, a sustainable micellar technology for the design and convenient synthesis of ligand-free oxidizable ultrasmall Pd(0) nanoparticles (NPs) and their subsequent catalytic exploration for couplings of water-sensitive acid chlorides in water is reported. A proline-derived amphiphile, PS-750-M, plays a crucial role in stabilizing these NPs, preventing their aggregation and oxidation state changes. These NPs were characterized using 13C nuclear magnetic resonance (NMR), infrared (IR), and surface-enhanced Raman scattering (SERS) spectroscopy to evaluate the carbonyl interactions of PS-750-M with Pd. High-resolution transmission electron microscopy (HRTEM) and energy-dispersive X-ray spectroscopy (EDX) studies were performed to reveal the morphology, particle size distribution, and chemical composition, whereas X-ray photoelectron spectroscopy (XPS) measurements unveiled the oxidation state of the metal. In the cross-couplings of water-sensitive acid chlorides with boronic acids, the micelle's shielding effect and boronic acids plays a vital role in preventing unwanted side reactions, including the hydrolysis of acid chlorides under basic pH. This approach is scalable and the applications are showcased in multigram scale reactions.

Bisulfite Addition Compounds as Substrates for Reductive Aminations in Water.

Highly valued products resulting from reductive aminations utilizing shelf-stable bisulfite addition compounds of aldehydes can be made under aqueous micellar catalysis conditions. Readily available α-picolineborane serves as the stoichiometric hydride source. Recycling of the aqueous reaction medium is easily accomplished, and several applications to targets in the pharmaceutical industry are documented.

Catalytic asymmetric and stereodivergent oligonucleotide synthesis.

We report the catalytic stereocontrolled synthesis of dinucleotides. We have demonstrated, for the first time to our knowledge, that chiral phosphoric acid (CPA) catalysts control the formation of stereogenic phosphorous centers during phosphoramidite transfer. Unprecedented levels of diastereodivergence have also been demonstrated, enabling access to either phosphite diastereomer. Two different CPA scaffolds have proven to be essential for achieving stereodivergence: peptide-embedded phosphothreonine-derived CPAs, which reinforce and amplify the inherent substrate preference, and C2-symmetric BINOL-derived CPAs, which completely overturn this stereochemical preference. The presently reported catalytic method does not require stoichiometric activators or chiral auxiliaries and enables asymmetric catalysis with readily available phosphoramidites. The method was applied to the stereocontrolled synthesis of diastereomeric dinucleotides as well as cyclic dinucleotides, which are of broad interest in immuno-oncology as agonists of the stimulator of interferon genes (STING) pathway.

Catalytic Sulfamoylation of Alcohols with Activated Aryl Sulfamates.

We report a new catalytic method for alcohol sulfamoylation that deploys electron-deficient aryl sulfamates as activated group transfer reagents. The reaction utilizes the simple organic base N-methylimidazole, proceeds under mild conditions, and provides intrinsic selectivity for 1° over 2° alcohols (up to >40:1 for certain nucleosides). The requisite aryl sulfamate donors are stable crystalline solids that can be readily prepared on a large scale. Mechanistic considerations support the intermediacy of HNSO2 "aza-sulfene" in the transfer reaction.

Competitive Workflow: novel software architecture for automating drug design.

As industrialization of laboratory processes for drug discovery continues to gather momentum, the bottleneck has moved toward exploitation of this tide of information to enable better quality decisions. The development of information-management systems to automate data and materials management can have a positive impact on productivity, as can increasingly sophisticated computer-aided molecular design approaches. However, as long as key decisions can only be taken by a small number of expert individuals working in a complex social environment, the impact of such innovations will be limited. This review describes Competitive Workflow, a distributed multi-agent system explicitly designed for the automation of decision making, currently the preserve of the expert. The approach builds on workflow architectures that capture best practice in information processing, but aims to extend these to model the tacit knowledge of the expert in the selection of alternative pathways through the workflow. The review also discusses recent developments in related workflow-management systems, particularly for information management and processing services front multiple sources, as well as distributed multi-agent approaches. A specific implementation of Competitive workflow--the Discovery Bus--and its application to meta-quantitative structure-activity relationship analysis is also described.

Discovery of Clinical Candidate 2-((2S,6S)-2-Phenyl-6-hydroxyadamantan-2-yl)-1-(3'-hydroxyazetidin-1-yl)ethanone [BMS-816336], an Orally Active Novel Selective 11ß-Hydroxysteroid Dehydrogenase Type 1 Inhibitor.

BMS-816336 (6n-2), a hydroxy-substituted adamantyl acetamide, has been identified as a novel, potent inhibitor against human 11ß-hydroxysteroid dehydrogenase type 1 (11ß-HSD1) enzyme (IC50 3.0 nM) with >10000-fold selectivity over human 11ß-hydroxysteroid dehydrogenase type 2 (11ß-HSD2). 6n-2 exhibits a robust acute pharmacodynamic effect in cynomolgus monkeys (ED50 0.12 mg/kg) and in DIO mice. It is orally bioavailable (%F ranges from 20 to 72% in preclinical species) and has a predicted pharmacokinetic profile of a high peak to trough ratio and short half-life in humans. This ADME profile met our selection criteria for once daily administration, targeting robust inhibition of 11ß-HSD1 enzyme for the first 12 h period after dosing followed by an "inhibition holiday" so that the potential for hypothalamic-pituitary-adrenal (HPA) axis activation might be mitigated. 6n-2 was found to be well-tolerated in phase 1 clinical studies and represents a potential new treatment for type 2 diabetes, metabolic syndrome, and other human diseases modulated by glucocorticoid control.

Integrating in vitro ADMET data through generic physiologically based pharmacokinetic models.

Early estimation of kinetics in man currently relies on extrapolation from experimental data generated in animals. Recent results from the application of a generic physiologically based model, Cloe PK) (Cyprotex), which is parameterised for human and rat physiology, to the estimation of plasma pharmacokinetics, are summarised in this paper. A comparison with predictive methods that involve scaling from in vivo animal data can also be made from recently published data. On average, the divergence of the predicted plasma concentrations from the observed data was 0.47 log units. For the external test set, > 70% of the predicted values of the AUC were within threefold of the observed values. Furthermore, the model was found to match or exceed the performance of three published interspecies scaling methods for estimating clearance, all of which showed a distinct bias towards overprediction. It is concluded that Cloe PK, as a means of integrating readily determined in vitro and/or in silico data, is a powerful, cost-effective tool for estimating exposure and kinetics in drug discovery and risk assessment that should, if widely adopted, lead to major reductions in the need for animal experimentation.

Laser induced mortality of Anopheles stephensi mosquitoes.

Small, flying insects continue to pose great risks to both human health and agricultural production throughout the world, so there remains a compelling need to develop new vector and pest control approaches. Here, we examined the use of short (<25 ms) laser pulses to kill or disable anesthetized female Anopheles stephensi mosquitoes, which were chosen as a representative species. The mortality of mosquitoes exposed to laser pulses of various wavelength, power, pulse duration, and spot size combinations was assessed 24 hours after exposure. For otherwise comparable conditions, green and far-infrared wavelengths were found to be more effective than near- and mid-infrared wavelengths. Pulses with larger laser spot sizes required lower lethal energy densities, or fluence, but more pulse energy than for smaller spot sizes with greater fluence. Pulse duration had to be reduced by several orders of magnitude to significantly lower the lethal pulse energy or fluence required. These results identified the most promising candidates for the lethal laser component in a system being designed to identify, track, and shoot down flying insects in the wild.

Tissue distribution of basic drugs: accounting for enantiomeric, compound and regional differences amongst beta-blocking drugs in rat.

The purpose of this research was to identify the major factors controlling the distribution of beta-blockers (acebutolol, betaxolol, bisoprolol, metoprolol, oxprenolol, pindolol, propranolol and timolol) in rats, across tissues, compounds and enantiomers. Tissue distribution was assessed at steady state by infusing cassette doses of beta-blockers into the jugular vein via an indwelling catheter at a constant rate. Blood was sampled via an indwelling catheter in the carotid artery, and 12 tissues excised at the end of dose infusion (4 or 8 h). Drug concentrations were quantified using a novel chiral LC-MS method and the tissue-to-plasma (Kp) and tissue-to-plasma water (Kpu) values were calculated for each tissue. Differences between Kp were observed between many enantiomeric pairs, and largely explained by enantiomeric differences in plasma protein binding. Across compounds, Kpu values were generally highest in lung and lowest in adipose, and were higher for the more lipophilic drugs betaxolol and propranolol. For any tissue, Kpu differences between the individual beta-blockers correlated well with the corresponding affinity for blood cells. For all compounds, regional tissue distribution correlated well with tissue acidic phospholipid concentrations, with phosphatidylserine appearing to have the strongest influence. This information may be used as the basis for predicting the tissue distribution of basic drugs.

Physiologically based pharmacokinetic modeling 1: predicting the tissue distribution of moderate-to-strong bases.

Tissue-to-plasma water partition coefficients (Kpu's) form an integral part of whole body physiologically based pharmacokinetic (WBPBPK) models. This research aims to improve the predictability of Kpu values for moderate-to-strong bases (pK(a) > or = 7), by developing a mechanistic equation that accommodates the unique electrostatic interactions of such drugs with tissue acidic phospholipids, where the affinity of this interaction is readily estimated from drug blood cell binding data. Additional model constituents are drug partitioning into neutral lipids and neutral phospholipids, and drug dissolution in tissue water. Major assumptions of this equation are that electrostatic interactions predominate, drugs distribute passively, and non-saturating conditions prevail. Resultant Kpu predictions for 28 moderate-to-strong bases were significantly more accurate than published equations with 89%, compared to 45%, of the predictions being within a factor of three of experimental values in rat adipose, bone, gut, heart, kidney, liver, muscle, pancreas, skin, spleen and thymus. Predictions in rat brain and lung were less accurate probably due to the involvement of additional processes not incorporated within the equation. This overall improvement in prediction should facilitate the further application of WBPBPK modeling, where time, cost and labor requirements associated with experimentally determining Kpu's have, to a large extent, deterred its application.

Progress in simulation modelling for pharmacokinetics.

Simulation models for the prediction of pharmacokinetics in humans and other mammalian species, which are based on the physiology and mechanistic models of absorption, distribution, metabolism and elimination are reviewed. The structure of such models is explained with reference to papers describing the mathematical details and alternative representations of organ flow and distribution. Approaches to the modelling of more complex tissues such as tumours and the liver are also reviewed as well as some specific transport processes such as biliary secretion and methods of ADME property estimation by experimental and in silico models. Specific approaches to the modelling of gastro-intestinal transit are explained as is the extension of the approach to simulating drug-drug interactions following co-administration of more than one drug.

Cross-validation pitfalls when selecting and assessing regression and classification models.

BACKGROUND: We address the problem of selecting and assessing classification and regression models using cross-validation. Current state-of-the-art methods can yield models with high variance, rendering them unsuitable for a number of practical applications including QSAR. In this paper we describe and evaluate best practices which improve reliability and increase confidence in selected models. A key operational component of the proposed methods is cloud computing which enables routine use of previously infeasible approaches. METHODS: We describe in detail an algorithm for repeated grid-search V-fold cross-validation for parameter tuning in classification and regression, and we define a repeated nested cross-validation algorithm for model assessment. As regards variable selection and parameter tuning we define two algorithms (repeated grid-search cross-validation and double cross-validation), and provide arguments for using the repeated grid-search in the general case. RESULTS: We show results of our algorithms on seven QSAR datasets. The variation of the prediction performance, which is the result of choosing different splits of the dataset in V-fold cross-validation, needs to be taken into account when selecting and assessing classification and regression models. CONCLUSIONS: We demonstrate the importance of repeating cross-validation when selecting an optimal model, as well as the importance of repeating nested cross-validation when assessing a prediction error.

Efficient and scalable enantioselective synthesis of a CGRP antagonist.

An enantioselective synthesis of the CGRP antagonist BMS-846372, amenable to large scale preparation, is presented. This new synthesis showcases a chemo- and enantioselective reduction of a cyclohepta[b]pyridine-5,9-dione as well as a Pd-catalyzed alpha-arylation reaction to form the key carbon-carbon bond and set the absolute and relative stereochemistry.