Organic Stereochemistry. Part 2

Host-guest complexation of cucurbit[7]uril and cucurbit[8]uril with the antimuscarinic drugs tropicamide and atropine

Cucurbiturils are useful excipients in eye drop formulations: they can increase the water solubility of the drug, enhance drug absorption into the eye, improve aqueous stability and reduce local irritation. Effective and safe drug delivery is, however, a challenge and the information on the host (CBs)/guest (tropicamide and atropine) interactions can help improving the existing treatments and develop novel therapies not limited only to eye diseases/conditions. Since this carrier system can easily modify the properties of the drug and ensure its delivery at the targeted ocular tissue, further insight into the intimate mechanism of the host-guest recognition is crucial. The present DFT/SMD study focuses on the role of numerous factors governing this process, namely the specific position of the guest molecule in the cavity of the cucurbituril, the ionization form (non/protonated) of the antimuscarinic drug, the dielectric constant of the medium, and the size of the cavitant pore. The obtained results are in line with experimental observations and shed light on the mechanism, at atomic resolution, of recognition between the CBs and the two parasympatholytic drugs.

The role of stereochemistry of antibiotic agents in the development of antibiotic resistance in the environment

Antibiotic resistance (ABR) is now recognised as a serious global health and economic threat that is most efficiently managed via a 'one health' approach incorporating environmental risk assessment. Although the environmental dimension of ABR has been largely overlooked, recent studies have underlined the importance of non-clinical settings in the emergence and spread of resistant strains. Despite this, several research gaps remain in regard to the development of a robust and fit-for-purpose environmental risk assessment for ABR drivers such as antibiotics (ABs). Here we explore the role the environment plays in the dissemination of ABR within the context of stereochemistry and its particular form, enantiomerism. Taking chloramphenicol as a proof of principle, we argue that stereoisomerism of ABs impacts on biological properties and the mechanisms of resistance and we discuss more broadly the importance of stereochemistry (enantiomerism in particular) with respect to antimicrobial potency and range of action.

Racemisation in Chemistry and Biology

The two enantiomers of a compound often have profoundly different biological properties and thus their liability to racemisation in aqueous solutions is an important piece of information. The authors reviewed the available data concerning the process of racemisation in vivo, in the presence of biological molecules (e.g., racemase enzymes, serum albumin, cofactors and derivatives) and under purely chemical but aqueous conditions (acid, base and other aqueous systems). Mechanistic studies are described critically in light of reported kinetic data. The types of experimental measurement that can be used to effectively determine rate constants of racemisation in various conditions are discussed and the data they provide is summarised. The proposed origins of enzymatic racemisation are presented and suggest ways to promote the process that are different from processes taking place in bulk water. Experimental and computational studies that provide understanding and quantitative predictions of racemisation risk are also presented.

The problem of racemization in drug discovery and tools to predict it

INTRODUCTION

Racemization has long been an ignored risk in drug development, probably because of a lack of convenient access to good tools for its detection and an absence of methods to predict racemization risk. As a result, the potential effects of racemization have been systematically underestimated. Areas covered: Herein, the potential effects of racemization are discussed through a review of drugs for which activity and side effects for both enantiomers are known. Subsequently, drugs known to racemize are discussed and the authors review methods to predict racemization risk. Application of a method quantitatively predicting racemization risk to databases of compounds from the medicinal chemistry literature shows that success in clinical trials is negatively correlated with racemization risk. Expert opinion: It is envisioned that a quantitative method of predicting racemization risk will remove a blind spot from the drug development pipeline. Removal of the blind spot will make drug development more efficient and result in less late-stage attrition of the drug pipeline.

A new fundamental type of conformational isomerism

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol^-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Isotope chirality in long-armed multifunctional organosilicon ("Cephalopod") molecules

Long-armed multifunctional organosilicon molecules display self-replicating and self-perfecting behavior in asymmetric autocatalysis (Soai reaction). Two representatives of this class were studied by statistical methods aiming at determination of probabilities of natural abundance chiral isotopomers. The results, reported here, show an astonishing richness of possibilities of the formation of chiral isotopically substituted derivatives. This feature could serve as a model for the evolution of biological chirality in prebiotic and early biotic stereochemistry.

Emergent chemodiversity: The case of stereoisomerism in acyclic alkanes

The objective of this pen-and-paper study is to witness the emergence of stereoisomeric properties when comparing lower to higher families of homologs. Specifically, the study compares all acyclic hexanes (five constitutional isomers, a.k.a. regioisomers), all nine heptanes, all 18 octanes, all 35 nonanes, and all 75 decanes. The first part of the work examines the nature and number of stereoisomeric properties seen to emerge in chemical structures featuring one chiral center (i.e., enantiomerism) or two such centers, in which case more complex stereoisomeric features emerge (enantiomerism, diastereoisomerism, pseudoasymmetry, and meso-isomers). The first emergence of chirality (i.e., enantiomerism) occurred in some heptanes. Diastereoisomerism and meso-isomers appear with some octanes, while a pseudoasymmetric center exists in a decane regioisomer. The second part of the work is an attempt to rationalize the numbers of regioisomers, chiral centers, and stereoisomers as these numbers grow from one family of regioisomers to the higher ones. Far from being random, such increases prove regular and ordered.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.

Types of stereoselectivity in drug metabolism: a heuristic approach

Stereochemical factors are known to play a significant role in the metabolism of drugs and other xenobiotics. Following Prelog's lead, types of metabolic stereoselectivity can be categorized as (i) substrate stereoselectivity (the differential metabolism of two or more stereoisomeric substrates) and (ii) product stereoselectivity (the differential formation of two or more stereoisomeric metabolites from a single substrate). Combinations of the two categories exist as (iii) substrate-product stereoselectivities, meaning that product stereoselectivity itself is substrate stereoselective. Here, published examples of metabolic stereoselectivities are examined in the light of these concepts. In parallel, a graphical scheme is presented with a view to facilitate learning and help researchers to solve classification problems.