Cyclic Peptide Design Guided by Residual Dipolar Couplings, J-Couplings, and Intramolecular Hydrogen Bond Analysis

Heterophyllin B: Combining Isotropic and Anisotropic NMR for the Conformational Analysis of a Natural Occurring Cyclic Peptide

Heterophyllin B is a natural occurring cyclic peptide with diverse attributed bioactivities. NMR-based conformational analysis of cyclic peptides often poses a challenge due to limited isotropic solution-state NMR data. In this study, we combined isotropic and anisotropic NMR observables including J-coupling, NOEs, amide proton temperature coefficients, and residual dipolar couplings (RDCs), which enabled the determination of a minimal conformational ensemble of heterophyllin B in methanol at density functional theory (DFT) accuracy. For conformational sampling of a cyclic peptide with a high degree of conformational freedom, we proposed a computational strategy that combines the Conformer-Rotamer Ensemble Sampling Tool (CREST) with the Commandline Energetic SOrting (CENSO). This combined computational and NMR-based approach offers a robust framework for the conformational analysis of cyclic peptides.

Discovery of Nirmatrelvir (PF-07321332): A Potent, Orally Active Inhibitor of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Main Protease

In early 2020, severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) infections leading to COVID-19 disease reached a global level leading to the World Health Organization (WHO) declaration of a pandemic. Scientists around the globe rapidly responded to try and discover novel therapeutics and repurpose extant drugs to treat the disease. This work describes the preclinical discovery efforts that led to the invention of PF-07321332 (nirmatrelvir, 14), a potent and orally active inhibitor of the SARS CoV-2 main protease (Mpro) enzyme. At the outset we focused on modifying PF-00835231 (1) discovered in 2004 as a potent inhibitor of the SARS CoV-1 Mpro with poor systemic exposure. Our effort was focused on modifying 1 with the goal of engineering in oral bioavailability by design, while maintaining cellular potency and low metabolic clearance. Modifications of 1 ultimately led to the invention of nirmatrelvir 14, the Mpro inhibitor component in PAXLOVID.

A comprehensive solute-medium interaction model for anisotropic NMR data prediction

Prediction of order parameters and hence anisotropic NMR data of a molecule dissolved in a dilute alignment medium can provide a unique means of solving certain challenging structural elucidation problems. Here, a comprehensive prediction model based on solute-medium interactions is developed featuring the use of medium-specific parameters as only fitting variables to depict intermolecular interactions in an alignment system, including repulsive, dispersive, and electrostatic interactions between the solute and the medium polymer, as well as their interactions with implicit solvent. This model is implemented on the framework of a surface decomposition method previously designed to formalize medium-induced solute alignment without a priori knowledge of the medium structure. Having descriptors for all interactions, the new model performs significantly better than the original hard-body model when the medium and solute exhibit strong electrostatic and dispersion interactions. This model offers a general method to extract the physical properties of a medium polymer by combining the experimental NMR data of different model compounds and then use these properties to predict the NMR data of other molecules of interest.

Cyclic Peptide C5aR1 Antagonist Design Using Solution Conformational Analysis Derived from Residual Dipolar Couplings

To gain further insight into the conformational properties of small cyclic peptides that bind to the G-protein coupled receptor C5aR1, we report here for the first time the elucidation of three peptide solution conformations using residual dipolar couplings and NMR temperature coefficients. Each of these peptides varies by at least one amino acid, adopts a different intramolecular hydrogen bonding pattern, and has a different solution conformation. The solution conformations were used in combination with a homology structure of C5aR1 as a design template for increasing the potency of peptide leads for the C5a receptor. This study provides a framework for using RDC solution conformations to guide the design of peptide mimetics that emulate the target bound state in solution to minimize the strain energy of the bound conformation and improve potency of the peptide for the target.

Structural basis for CCR6 modulation by allosteric antagonists

The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation. Here, we present two inactive CCR6 structures in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. The oxomorpholine analogues, OXM1 and OXM2 are highly selective CCR6 antagonists which bind to an extracellular pocket and disrupt the receptor activation network. An energetically favoured U-shaped conformation in solution that resembles the bound form is observed for the active analogues. SQA1 is a squaramide derivative with close-in analogues reported as antagonists of chemokine receptors including CCR6. SQA1 binds to an intracellular pocket which overlaps with the G protein site, stabilizing a closed pocket that is a hallmark of inactive GPCRs. Minimal communication between the two allosteric pockets is observed, in contrast to the prevalent allosteric cooperativity model of GPCRs. This work highlights the versatility of GPCR antagonism by small molecules, complementing previous knowledge of CCR6 activation, and sheds light on drug discovery targeting CCR6.

Cryogen-free 400-MHz nuclear magnetic resonance spectrometer as a versatile tool for pharmaceutical process analytical technology

The discovery of new ceramic materials containing Ba-La-Cu oxides in 1986 that exhibited superconducting properties at high temperatures in the range of 35 K or higher, recognized with the Nobel Prize in Physics in 1987, opened a new world of opportunities for nuclear magnetic resonance (NMRs) and magnetic resonance imaging (MRIs) to move away from liquid cryogens. This discovery expands the application of high temperature superconducting (HTS) materials to fields beyond the chemical and medical industries, including electrical power grids, energy, and aerospace. The prototype 400-MHz cryofree HTS NMR spectrometer installed at Amgen's chemistry laboratory has been vital for a variety of applications such as structure analysis, reaction monitoring, and CASE-3D studies with RDCs. The spectrometer has been integrated with Amgen's chemistry and analytical workflows, providing pipeline project support in tandem with other Kinetic Analysis Platform technologies. The 400-MHz cryofree HTS NMR spectrometer, as the name implies, does not require liquid cryogens refills and has smaller footprint that facilitates installation into a chemistry laboratory fume hood, sharing the hood with a process chemistry reactor. Our evaluation of its performance for structural analysis with CASE-3D protocol and for reaction monitoring of Amgen's pipeline chemistry was successful. We envision that the HTS magnets would become part of the standard NMR and MRI spectrometers in the future. We believe that while the technology is being developed, there is room for all magnet options, including HTS, low temperature superconducting (LTS) magnets, and low field benchtop NMRs with permanent magnets, where utilization will be dependent on application type and costs.

Discovery of the Potent and Selective MC4R Antagonist PF-07258669 for the Potential Treatment of Appetite Loss

The melanocortin-4 receptor (MC4R) is a centrally expressed, class A GPCR that plays a key role in the regulation of appetite and food intake. Deficiencies in MC4R signaling result in hyperphagia and increased body mass in humans. Antagonism of MC4R signaling has the potential to mitigate decreased appetite and body weight loss in the setting of anorexia or cachexia due to underlying disease. Herein, we report on the identification of a series of orally bioavailable, small-molecule MC4R antagonists using a focused hit identification effort and the optimization of these antagonists to provide clinical candidate 23. Introduction of a spirocyclic conformational constraint allowed for simultaneous optimization of MC4R potency and ADME attributes while avoiding the production of hERG active metabolites observed in early series leads. Compound 23 is a potent and selective MC4R antagonist with robust efficacy in an aged rat model of cachexia and has progressed into clinical trials.

Residual Dipolar Coupling Based Conformational Analysis Allows the Configurational Assessment of Steroids with up to Eight Stereocenters

Residual dipolar couplings (RDCs) induced by anisotropic media have been proved as a powerful tool for the structure elucidation of organic molecules in solution in nuclear magnetic resonance (NMR) based analysis. The value of dipolar couplings to solve complex conformational and configurational problems represents indeed an appealing analytical tool for the pharmaceutical industry particularly focusing on the stereochemistry characterization of NCEs since the early phase of the drug development process. In our work, RDCs were used for the conformational and configurational study of synthetic steroids with multiple stereocenters - prednisone and beclomethasone dipropionate (BDP) -. For both molecules the correct relative configuration was identified among all the possible diastereoisomers (32 and 128 respectively) arising from the compounds stereogenic carbons. Only for prednisone the use of additional experimental data (i. e. rOes) was necessary to resolve the right stereochemical structure.

Pushing the Limits of Characterising a Weak Halogen Bond in Solution

Detection and characterisation of very weak, non-covalent interactions in solution is inherently challenging. Low affinity, short complex lifetime and a constant battle against entropy brings even the most sensitive spectroscopic methods to their knees. Herein we introduce a strategy for the accurate experimental description of weak chemical forces in solution. Its scope is demonstrated by the detailed geometric and thermodynamic characterisation of the weak halogen bond of a non-fluorinated aryl iodide and an ether oxygen (0.6 kJ mol-1 ). Our approach makes use of the entropic advantage of studying a weak force intramolecularly, embedded into a cooperatively folding system, and of the combined use of NOE- and RDC-based ensemble analyses to accurately describe the orientation of the donor and acceptor sites. Thermodynamic constants (ΔG, ΔH and ΔS), describing the specific interaction, were derived from variable temperature chemical shift analysis. We present a methodology for the experimental investigation of remarkably weak halogen bonds and other related weak forces in solution, paving the way for their improved understanding and strategic use in chemistry and biology.

Cross-Linked Poly-4-Acrylomorpholine: A Flexible and Reversibly Compressible Aligning Gel for Anisotropic NMR Analysis of Peptides and Small Molecules in Water

Determination of the solution conformation of both small organic molecules and peptides in water remains a substantial hurdle in using NMR solution conformations to guide drug design due to the lack of easy to use alignment media. Herein we report the design of a flexible compressible chemically cross-linked poly-4-acrylomorpholine gel that can be used for the alignment of both small molecules and cyclic peptides in water. To test the new gel, residual dipolar couplings (RDCs) and J-coupling constants were used in the configurational analysis of strychnine hydrochloride, a molecule that has been studied extensively in organic solvents as well as a small cyclic peptide that is known to form an α-helix in water. The conformational ensembles for each molecule with the best fit to the data are reported. Identification of minor conformers in water that cannot easily be determined by conventional NOE measurements will facilitate the use of RDC experiments in structure-based drug design.

NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview

BACKGROUND

NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems.

OBJECTIVE

This review provides a toolkit to investigate peptide conformational properties by NMR.

METHODS

Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well.

RESULTS

The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well.

CONCLUSION

NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

Improvement on Permeability of Cyclic Peptide/Peptidomimetic: Backbone N-Methylation as A Useful Tool

Peptides have a three-dimensional configuration that can adopt particular conformations for binding to proteins, which are well suited to interact with larger contact surface areas on target proteins. However, low cell permeability is a major challenge in the development of peptide-related drugs. In recent years, backbone N-methylation has been a useful tool for manipulating the permeability of cyclic peptides/peptidomimetics. Backbone N-methylation permits the adjustment of molecule’s conformational space. Several pathways are involved in the drug absorption pathway; the relative importance of each N-methylation to total permeation is likely to differ with intrinsic properties of cyclic peptide/peptidomimetic. Recent studies on the permeability of cyclic peptides/peptidomimetics using the backbone N-methylation strategy and synthetic methodologies will be presented in this review.

Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters

The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D₂ O, DMSO-d₆ , CDCl₃ , and C₆ D₆ ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D₂ O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl₃ and C₆ D₆ , and a poly (hydroxyethyl methacrylate) gel for DMSO-d₆ . Whereas the pyrrolizidine ring shows an E₆ exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.

Flexibility and Cell Permeability of Cyclic Ras-Inhibitor Peptides Revealed by the Coupled Nosé-Hoover Equation

Quantifying the cell permeability of cyclic peptides is crucial for their rational drug design. However, the reasons remain unclear why a minor chemical modification, such as the difference between Ras inhibitors cyclorasin 9A5 and 9A54, can substantially change a peptide's permeability. To address this question, we performed enhanced sampling simulations of these two 11-mer peptides using the coupled Nosé-Hoover equation (cNH) we recently developed. The present cNH simulations realized temperature fluctuations over a wide range (240-600 K) in a dynamic manner, allowing structural samplings that were well validated by nuclear Overhauser effect measurements. The derived structural ensembles were comprehensively analyzed by all-atom structural clustering, mapping the derived clusters onto principal components (PCs) that characterize the cyclic structure, and calculating cluster-dependent geometric and chemical properties. The planar-open conformation was dominant in aqueous solvent, owing to inclusion of the Trp side chain in the main-chain ring, while the compact-closed conformation, which favors cell permeation due to its compactness and high polarity, was also accessible. Conformation-dependent cell permeability was observed in one of the derived PCs, demonstrating that decreased cell permeability in 9A54 is due to the high free energy barrier separating the two conformations. The origin of the change in free energy surface was determined to be loss of flexibility in the modified residues 2-3, resulting from the increased bulkiness of their side chains. The derived molecular mechanism of cell permeability highlights the significance of complete structural dynamics surveys for accelerating drug development with cyclic peptides.

NMR spectroscopy: the swiss army knife of drug discovery

Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool within drug discovery over the last two decades. While traditionally being used by medicinal chemists for small molecule structure elucidation, it can also be a valuable tool for the identification of small molecules that bind to drug targets, for the characterization of target-ligand interactions and for hit-to-lead optimization. Here, we describe how NMR spectroscopy is integrated into the Pfizer drug discovery pipeline and how we utilize this approach to identify and validate initial hits and generate leads.

Selective Nuclear Magnetic Resonance Experiments for Sign-Sensitive Determination of Heteronuclear Couplings: Expanding the Analysis of Crude Reaction Mixtures

State-of-the-art nuclear magnetic resonance (NMR) selective experiments are capable of directly analyzing crude reaction mixtures. A new experiment named HD-HAPPY-FESTA yields ultrahigh-resolution total correlation subspectra, which are suitable for sign-sensitive determination of heteronuclear couplings, as demonstrated here by measuring the sign and magnitude for proton-fluorine couplings (J_HF) from major and minor isomer products of a two-step reaction without any purification. Proton-fluorine couplings ranging from 51.5 to -2.6 Hz could be measured using HD-HAPPY-FESTA, with the smallest measured magnitude of 0.8 Hz. Experimental J_HF values were used to identify the two fluoroketone intermediates and the four fluoroalcohol products. Results were rationalized and compared with the density functional theory (DFT) calculations. Experimental data were further compared with the couplings reported in the literature, where pure samples were analyzed.

Structure-Property Relationship Study of N-(Hydroxy)Peptides for the Design of Self-Assembled Parallel β-Sheets

The design of novel and functional biomimetic foldamers remains a major challenge in creating mimics of native protein structures. Herein, we report the stabilization of a remarkably short β-sheet by incorporating N-(hydroxy)glycine (Hyg) residues into the backbone of peptides. These peptide-peptoid hybrids form unique parallel β-sheet structures by self-assembly upon hydrogenation. Our spectroscopic and crystallographic data suggest that the local conformational perturbations induced by N-(hydroxy)amides are outweighed by a network of strong interstrand hydrogen bonds.