Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

To unravel the relationship between the European wild apple, Malus sylvestris (L.) Mill., and its domesticated relative M. domestica Borkh., we studied chloroplast DNA variation in 634 wild and 422 domesticated accessions originating from different regions. Hybridization between M. sylvestris and M. domestica was checked using 10 nuclear microsatellites and a Bayesian assignment approach. This allowed us to identify hybrids and feral plants escaped from cultivation. Sixty-eight genotypes belonging to 12 other wild Malus species, including 20 M. sieversii (Ledeb.) Roem. accessions were also included in the analysis of chloroplast diversity. Marker techniques were developed to type a formerly described duplication and a newly detected transversion in the matK gene. Chloroplast DNA variation was further investigated using PCR-RFLP (Polymerase Chain Reaction-Random Fragment Length Polymorphism), and haplotypes were constructed based on all mutational combinations. A closer relationship than presently accepted between M. sylvestris and M. domestica was established at the cytoplasmic level, with the detection of eight chloroplast haplotypes shared by both species. Hybridization between M. sylvestris and M. domestica was also apparent at the local level with sharing of rare haplotypes among local cultivars and sympatric wild trees. Indications of the use of wild Malus genotypes in the (local) cultivation process of M. domestica and cytoplasmic introgression of chloroplast haplotypes into M. sylvestris from the domesticated apple were found. Only one of the M. sieversii trees studied displayed one of the three main chloroplast haplotypes shared by M. sylvestris and M. domestica. This is surprising as M. sieversii has formerly been described as the main maternal progenitor of the domesticated apple. This study hereby reopens the exciting discussion on the origin of M. domestica.

The aim of the present study was to investigate the genetic variation in Danish populations of the endangered European crab apple (Malus sylvestris). Special emphasis was given to hybridization between the wild species and its cultivated relative Malus ×domestica. A total of 178 wild individuals from four Danish populations were studied along with a reference sample of 29 old cultivars. The genetic variation within and among samples was studied at ten microsatellite marker loci. Additionally, a morphological analysis was carried out to identify hybrids and test for correspondence between phenotypic and genotypic indices of hybridization.From application of ordination and a model based cluster analysis to the molecular data, two clusters were identified consisting of wild and cultivated individuals respectively. This indicates that pronounced admixture between the two species is not present. At the population level, a high correspondence was found between geographic isolation from M. ×domestica and genotypic and morphological indices of hybridization. As expected, isolated populations appeared less affected by hybridization than poorly isolated populations. Isolated 'pure' M. sylvestris populations could thus be identified. However, morphological and molecular evidence of hybridization was found to be divergent at the individual level. This is suggestive of some historical introgression into the M. sylvestris gene pool, and indicates that relying exclusively on either morphological or molecular characters as diagnostic markers in studies of hybridization between M. ×domestica and M. sylvestris might lead to fallible results. Combined application of genetic and morphological markers is therefore recommended.3

Abstract• Hybridization and mating pattern between Quercus robur and Q. petraea was studied in a 5.8 ha mixed forest stand in Jutland, Denmark which comprises in total 135 Quercus robur and 230 Q. petraea trees. Classification of the oak trees into species was performed using canonical discriminant analysis of a range of leaf morphological traits. Adult trees (365) and offspring (582) were genotyped with eight microsatellite markers. Seedlings were sampled in 2003 and acorns were collected in 2004.• Mating patterns of Q. robur and Q. petraea are expected to be different in the northern range of the distribution area and a larger hybridization rate is expected. It is further expected, that pollination from outside sources will be relatively less in small fragmented forest management systems compared to large scale oak forest. The conclusions should be verified through repeated year to year analysis of the mating pattern.• Phenological studies revealed that there was no difference in flowering time between species. Data for the adult trees revealed no significant departures from Hardy-Weinberg proportions and there was weak, but significant spatial genetic structure, which supports the idea that the stand is of natural origin. Spatial genetic structure in the first distance class is stronger for Q. petraea. The genetic composition of the offspring was remarkably consistent from year to year. Paternity analysis revealed that, on average, 85% pollination came from fathers within the stand. The direction of the pollen flow varied from year to year. Inter-specific hybridization was high and ranged from 15-17% and from 48-55% for Q. petraea and Q. robur mothers respectively. Paternity analysis revealed that the population was basically outcrossing and only 3.7% of the analysed progeny were the product of selfing. Over the two years of study, approximately 200 trees contributed to the paternity of the next generations.• The study confirms earlier studies with a greater tendency for Q. robur mothers to produce hybrid seeds than Q. petraea mothers. The rate of hybridization is higher in this Danish stand than in comparable studies elsewhere in Europe. Gene flow from outside sources are relatively low. • Des études phénologiques montrent qu'il n'y a pas de différence entre les espèces pour la période de floraison. Les données sur arbres adultes ne révèlent aucun écart significatif par rapport aux proportions attendues de la loi de Hardy-Weinberg. Une structuration spatiale faible mais significative a été mise en évidence, qui suggère l'idée que le peuplement est d'origine naturelle. Cette structuration est plus forte pour Q. petraea. La composition génétique des descendances est remarquablement stable d'une année sur l'autre. Les analyses de paternité révèlent qu'en moyenne 85 % de la pollinisation provient de pères du peuplement. Le sens de pollinisation varie d'une année sur l'autre. Le taux d'hybrides interspécifiques est élevé et varie de 15-17 % et de 48-55 % respectivement pour Q. petraea et Q. robur. Les études de p...

Pollen mediated gene flow was studied in a Danish population of Malus sylvestris with the objective to support the Danish genetic conservation and management activities. A total of 50 mature trees (potential pollen donors) along with 180 seedlings (originating from 12 of the mature trees) were genotyped at 10 nuclear microsatellite loci. Paternity could be established for 46 seedlings, and a pollination distribution curve based on these observations was developed. Further, two indirect methods, KINDIST and TWOGENER were applied for estimation of gene flow parameters. Pollinations were mostly between nearby trees with a median of observed pollination distances of approximately 23 m. However, a few long distance pollinations were observed and this increased the average pollination distance to approximately 60 m. The KINDIST analysis of the data seemed to underestimate the average pollination distance as the fat-tailed distribution of the pollen dispersal distribution was not taken into account. Application of the results in a conservation and domestication context is discussed.

We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.

Dehydration of crystalline solids is a widespread phenomenon, yet the fundamental mechanisms by which dehydration occurs are not properly understood. This arises due to technical limitations in studying such fast processes with sufficient sensitivity; nevertheless, understanding dehydration pathways is critical for designing optimal properties for materials, particularly in the case of pharmaceutical solids. The computational methods presented here allow for accurate determination of the dehydrated species’ crystal structure and to develop an understanding of the mechanism of dehydration at the molecular level. This work also highlights the critical role of explicitly taking into account the dynamical aspect of molecules using computational techniques, rather than relying on static energy minimization approaches. Specifically, the crystalline active pharmaceutical agent naproxen sodium, and its hydrates, is studied in silico using density functional theory and molecular dynamics, ultimately elucidating the face-specific dehydration mechanisms and revealing highly complex diffusion and nucleation behavior. Additionally, the results indicate that the method is a viable way to explore dehydration pathways and predict new dehydrated crystal structures.

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.