Understanding molecular self-association in solution is vital for uncovering polymorph-selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of p-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and supersaturation conditions. NMR reveals that dominant interactions stabilizing pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π–π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallization is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concentrationsconditions that are known to yield crystals of the β formcarboxylic–carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallization is known to yield the α forma small but statistically significant fraction of symmetric carboxylic–carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the symmetric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway toward the nucleation of α-pABA.

<div><div><div><p>Understanding molecular self-association in solution is vital for uncovering polymorph- selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of para-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and su- persaturation conditions. NMR reveals that dominant interactions stabilising pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π - π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallisation is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concen- trations - conditions that are known to yield crystals of the β form - carboxylic-carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallisation is known to yield the α form - a small but statistically significant fraction of symmetric carboxylic-carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the sym- metric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway towards the nucleation of α-pABA.</p></div></div></div>

Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here, we explore the selectivity-determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors and describe the critical transition states in atomistic resolution. The simulation results are compared with experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such a behavior is not observed for several other aspartic proteases. The ability to estimate the selectivity of compounds before they are synthesized is of considerable importance in drug design; therefore, we expect that our approach will be useful in selective inhibitor designs against not only aspartic proteases but also other enzyme classes.

Prenucleation aggregates are important species in the crystallization pathway. Here, we combine heteronuclear Overhauser effect spectroscopy (HOESY) and molecular dynamics calculations to study solute molecule association in a model systembenzoic acid/pentafluorobenzoic acid. Our findings indicate that HOEs arise from diffusion-limited prenucleation aggregates and that association is solvent dependent.

<div><div><div><p>Understanding molecular self-association in solution is vital for uncovering polymorph- selective crystal nucleation pathways. In this paper, we combine solution NMR spectroscopy and molecular dynamics simulations to shed light on the structural and dynamical features of para-aminobenzoic acid (pABA) in solution, and on their role in pABA crystals nucleation. pABA is known to yield different crystal forms (α, and β) depending on solvent choice and su- persaturation conditions. NMR reveals that dominant interactions stabilising pABA oligomers are markedly solvent-dependent: in organic solvents, hydrogen bonds dominate, while water promotes π - π stacking. Despite this clear preference, both types of interactions contribute to the variety of self-associated species in all solvents considered. MD simulations support this observation and show that pABA oligomers are short-lived and display a fluxional character, therefore indicating that the growth unit involved in pABA crystallisation is likely to be a single molecule. Nevertheless, we note that the interactions dominating in pABA oligomers are indicative of the polymorph obtained from precipitation. In water, at low pABA concen- trations - conditions that are known to yield crystals of the β form - carboxylic-carboxylic hydrogen bonds are exclusively asymmetric. At higher pABA concentration conditions in which the crystallisation is known to yield the α form - a small but statistically significant fraction of symmetric carboxylic-carboxylic hydrogen-bonded dimers is present. We interpret the presence of these interactions in solvated pABA oligomers as indicative of the fact that a simultaneous and complete desolvation of two carboxylic groups, necessary to form the sym- metric hydrogen-bonded dimer typical of the α crystal form, is accessible, therefore directing the nucleation pathway towards the nucleation of α-pABA.</p></div></div></div>

Pre-nucleation aggregates are important species on the crystallisation pathway. Here we combine heteronuclear Overhauser effect spectroscopy (HOESY) and molecular dynamics calculations to study the self-association of a model system – benzoic acid. Our findings indicate that heteronuclear Overhauser effects arise from diffusion-limited pre-nucleation aggregates and that self-association is solvent dependant.

Selectivity is a major issue in the development of drugs targeting pathogen aspartic proteases. Here we explore the selectivity determining factors by studying specifically designed malaria aspartic protease (plasmepsin) open-flap inhibitors. Metadynamics simulations are used to uncover the complex binding/unbinding pathways of these inhibitors, and describe the critical transition states in atomistic resolution. The simulation results are compared to experimentally determined enzymatic activities. Our findings demonstrate that plasmepsin inhibitor selectivity can be achieved by targeting the flap loop with hydrophobic substituents that enable ligand binding under the flap loop, as such behaviour is not observed for several other aspartic proteases. The ability to estimate compound selectivity before they are synthesized is of great importance in drug design, therefore, we expect that our approach will be useful in selective inhibitor design not only against aspartic proteases, but other enzyme classes as well.

Pre-nucleation aggregates are important species on the crystallisation pathway. Here we combine heteronuclear Overhauser effect spectroscopy (HOESY) and molecular dynamics calculations to study the self-association of a model system – benzoic acid. Our findings indicate that heteronuclear Overhauser effects arise from diffusion-limited pre-nucleation aggregates and that self-association is solvent dependant.