Molecular docking is a popular computational tool in drug discovery. Leveraging structural information, docking software predicts binding poses of small molecules to cavities on the surfaces of proteins. Virtual screening for ligand discovery is a useful application of docking software. In this chapter, using the enigmatic KRAS protein as an example system, we endeavor to teach the reader about best practices for performing molecular docking with UCSF DOCK. We discuss methods for virtual screening and docking molecules on KRAS. We present the following six points to optimize our docking setup for prosecuting a virtual screen: protein structure choice, pocket selection, optimization of the scoring function, modification of sampling spheres and sampling procedures, choosing an appropriate portion of chemical space to dock, and the choice of which top scoring molecules to pick for purchase.

Dedicator of cytokinesis 10 (DOCK10), an evolutionarily conserved guanine nucleotide exchange factor (GEF) for Rho GTPases, has the unique specificity within the DOCK-D subfamily to activate both Cdc42 and Rac, but the structural bases for these activities remained unknown. Here we present the crystal structures of the catalytic DHR2 domain of mouse DOCK10, complexed with either Cdc42 or Rac1. The structures revealed that DOCK10DHR2 binds to Cdc42 or Rac1 by slightly changing the arrangement of its two catalytic lobes. DOCK10 also has a flexible binding pocket for the 56th GTPase residue, allowing a novel interaction with Trp56Rac1. The conserved residues in switch 1 of Cdc42 and Rac1 showed common interactions with the unique Lys-His sequence in the β5/β6 loop of DOCK10DHR2. However, the interaction of switch 1 in Rac1 was less stable than that of switch 1 in Cdc42, due to amino acid differences at positions 27 and 30. Structure-based mutagenesis identified the DOCK10 residues that determine the Cdc42/Rac1 dual specificity.

Dedicator of cytokinesis 2 (DOCK2) can activate the downstream small G protein Rac and regulate cytoskeletal reorganization. DOCK2 is essential for critical physiological processes such as migration, activation, proliferation, and effects of immune cells, including lymphocytes, neutrophils, macrophages, and dendritic cells. For example, DOCK2 is involved in the development and activation of T and B lymphocytes by affecting synapse formation and inhibiting the development of the Th2 lineage by downregulating IL-4Rα surface expression. Not only that, DOCK2 may be a molecular target for controlling cardiac transplant rejection and Alzheimer\'s disease (AD). Patients with defects in the DOCK2 gene also exhibit a variety of impaired cellular functions, such as chemotactic responses of lymphocytes and reactive oxygen species (ROS) production by neutrophils. To date, DOCK2 has been shown to be involved in the development of various diseases, including AD, pneumonia, myocarditis, colitis, tumors, etc. DOCK2 plays different roles in these diseases and the degree of inflammatory response has a different impact on the progression of disease. In this paper, we present a review of recent advances in the function of DOCK2 in various immune cells and its role in various diseases.

In recent years, the prevalence and mortality of autism spectrum disorder (ASD) have been increasing. The clinical features are different with different cases, so the treatment ways are different for each one.
Baohewan Heshiwei Wen Dan Tang (BHWDT) has been recommended for treating autistic spectrum disorder. To investigate the mechanism of action and how the compounds interact with ASD targets, network pharmacology and molecular docking methods were used in this study.
Traditional Chinese Medicine Systems Pharmacology (TCMSP) was used to screen the active components according to index of oral bio-activity and drug-likeness. Then, TCMSP and Swiss Target Prediction databases were used to screen potential target genes of active components. The related target genes of ASD were obtained from the Gene Cards database. Matescape database was utilized to get gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation of gene targets. Composition- target-pathway (C-T-P) and a protein-protein interaction (PPI) networks were built with Cytoscape 3.8.2 software.
The interaction of the main active components of BHWDT was verified by molecular docking. The key targets of MAPK1, IL6, CXCL8 and TP53 of BHWDT were obtained. The key active components Quercetin, Kaempferol and Iuteolin of BHWDT could bind with MAPK1, IL6, CXCL8 and TP53 of BHWDT, respectively.
BHWDT can be highly effective for treating ASD and this study can help us to understand multiple targets and multiple pathways mechanism.

As a complement to virtual screening, de novo design of small molecules is an alternative approach for identifying potential drug candidates. Here, we present a new 3D genetic algorithm to evolve molecules through breeding, mutation, fitness pressure, and selection. The method, termed DOCK_GA, builds upon and leverages powerful sampling, scoring, and searching routines previously implemented into DOCK6. Three primary experiments were used during development: Single-molecule evolution evaluated three selection methods (elitism, tournament, and roulette), in four clinically relevant systems, in terms of mutation type and crossover success, chemical properties, ensemble diversity, and fitness convergence, among others. Large scale benchmarking assessed performance across 651 different protein-ligand systems. Ensemble-based evolution demonstrated using multiple inhibitors simultaneously to seed growth in a SARS-CoV-2 target. Key takeaways include: (1) The algorithm is robust as demonstrated by the successful evolution of molecules across a large diverse dataset. (2) Users have flexibility with regards to parent input, selection method, fitness function, and molecular descriptors. (3) The program is straightforward to run and only requires a single executable and input file at run-time. (4) The elitism selection method yields more tightly clustered molecules in terms of 2D/3D similarity, with more favorable fitness, followed by tournament and roulette.

Human epidermal growth factor receptor 2 (HER2) is an oncogenic driver and key therapeutic target for human cancers. Current therapies targeting HER2 are primarily based on overexpression of the wild-type form of HER2. However, kinase domain mutations have been identified that can increase the activity of HER2 even when expressed at basal levels. Using purified enzymes, we confirmed the hyperactivity of two HER2 mutants (D769Y and P780insGSP). To identify small molecule inhibitors against these cancer-associated variants, we used a combined approach consisting of biochemical testing, similarity-based searching, and in silico modeling. These approaches resulted in the identification of a candidate molecule that inhibits mutant forms of HER2 in vitro and in cell-based assays. Our structural model predicts that the compound takes advantage of water-mediated interactions in the HER2 kinase binding pocket.

The Dedicator of Cytokinesis (DOCK) family (DOCK1-11) of genes are essential mediators of cellular migration, growth, and fusion in a variety of cell types and tissues. Recent advances in whole-genome sequencing of patients with undiagnosed genetic disorders have identified several rare pathogenic variants in DOCK genes. We conducted a systematic review and performed a patient database and literature search of reported DOCK pathogenic variants that have been identified in association with clinical pathologies such as global developmental delay, immune cell dysfunction, muscle hypotonia, and muscle ataxia among other categories. We then categorized these pathogenic DOCK variants and their associated clinical phenotypes under several unique categories: developmental, cardiovascular, metabolic, cognitive, or neuromuscular. Our systematic review of DOCK variants aims to identify and analyze potential DOCK-regulated networks associated with neuromuscular diseases and other disease pathologies, which may identify novel therapeutic strategies and targets. This systematic analysis and categorization of human-associated pathologies with DOCK pathogenic variants is the first report to the best of our knowledge for a unique class in this understudied gene family that has important implications in furthering personalized genomic medicine, clinical diagnoses, and improve targeted therapeutic outcomes across many clinical pathologies.

Today, more than ever, the search for non-trivial sources of biologically active substances is critical. Plants of the genus Rumex are noteworthy. Plants of this genus stand out for a number of advantages from the dominant plant core of meadow phytocenoses of the temperate climatic zone: a short growing season, an intensive increase in biomass, and undemanding growth conditions. In addition, this plant genus is known as a super-producer of secondary phenolic compounds. The wide distribution and intensive synthesis of biologically active substances make plants from the genus Rumex a promising object for study. Seven species of the genus Rumex (R. acetosa, R. acetosella, R. confertus, R. crispus, R. maritimus, R.obtusifolius, and R. sanguineus) were analyzed. Plants were collected under relatively uniform growing conditions. For subsequent extraction and analysis of phenolic compounds, as well as antioxidant activity, plants leaves were used. R. acetosella, R. crispus, R. maritimus, R. obtusifolius, and R. sanguineus were characterized by a high total content of phenolic compounds (111-131 mg g-1). The maximum content of flavonoids was found in the leaves of R. maritimus and R. acetosella. At the same time, according to high-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis, derivatives of flavones (apigenin and luteolin) predominated in the leaves of R. acetosella, while in other species, mainly derivatives of flavonols (quercetin and kaempferol) were identified. Plants of R. acetosa, in comparison with other studied species, were characterized by a lower content of the studied groups of phenolic compounds, with the exception of hydroxycinnamic acids, the content of which in this species was comparable to the content of flavonoids. The maximum content of catechins was found in R. sanguineus; proanthocyanidins-in R. sanguineus, R. obtusifolius, and R. crispus; and tannins-in R. obtusifolius. Extracts from R. crispus were characterized by high antioxidant activity, measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2\'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), and ferric reducing antioxidant power (FRAP) assays. In addition, the assessment of the phenolic profile of the plant made it possible to group the plants within the framework of cluster analysis. The distribution pattern in the clusters corresponded to the generally accepted taxonomy, with a characteristic division into subgenera (Acetosa, Acetosella, and Rumex). Thus, the phenolic profile can be considered as an additional instrumental approach when drawing up a systematic hierarchy.

Multicellular organisms use dedicator of cytokinesis (DOCK) family guanine nucleotide exchange factors (GEFs) to activate Rac/Rho-of-plants small GTPases and coordinate cell shape change. In developing tissues, DOCK signals integrate cell-cell interactions with cytoskeleton remodeling, and the GEFs cluster reversibly at specific organelle surfaces to orchestrate cytoskeletal reorganization. The domain organizations among DOCK orthologs are diverse, and the mechanisms of localization control are poorly understood. Here, we use combinations of transgene complementation and live-cell imaging assays to uncover an evolutionarily conserved and essential localization determinant in the DOCK-GEF named SPIKE1. The SPIKE1-DHR3 domain is sufficient for organelle association in vivo, and displays a complicated lipid-binding selectivity for both phospholipid head groups and fatty acid chain saturation. SPIKE1-DHR3 is predicted to adopt a C2-domain structure and functions as part of a tandem C2 array that enables reversible clustering at the cell apex. This work provides mechanistic insight into how DOCK GEFs sense compositional and biophysical membrane properties at the interface of two organelle systems.

Rho family guanosine triphosphatases (GTPases) regulate cellular signaling and cytoskeletal dynamics, playing a pivotal role in cell adhesion, migration, and cell cycle progression. The Rac subfamily of Rho GTPases consists of three highly homologous proteins, Rac 1-3. The proper function of Rac1 and Rac3, and their correct interaction with guanine nucleotide-exchange factors (GEFs) and GTPase-activating proteins (GAPs) are crucial for neural development. Pathogenic variants affecting these delicate biological processes are implicated in different medical conditions in humans, primarily neurodevelopmental disorders (NDDs). In addition to a direct deleterious effect produced by genetic variants in the RAC genes, a dysregulated GTPase activity resulting from an abnormal function of GEFs and GAPs has been involved in the pathogenesis of distinctive emerging conditions. In this study, we reviewed the current pertinent literature on Rac-related disorders with a primary neurological involvement, providing an overview of the current knowledge on the pathophysiological mechanisms involved in the neuro-RACopathies.