Retrieval Augmented Docking Using Hierarchical Navigable Small Worlds

Make-on-demand chemical libraries have drastically increased the reach of molecular docking, with the enumerated ready-to-dock ZINC-22 library approaching 6.4 billion molecules (July 2024). While ever-growing libraries result in better-scoring molecules, the computational resources required to dock all of ZINC-22 make this endeavor infeasible for most. Here, we organize and traverse chemical space with hierarchical navigable small-world graphs, a method we term retrieval augmented docking (RAD). RAD recovers most virtual actives, despite docking only a fraction of the library. Furthermore, RAD is protein-agnostic, supporting additional docking campaigns without additional computational overhead. In depth, we assess RAD on published large-scale docking campaigns against D4 and AmpC spanning 99.5 million and 138 million molecules, respectively. RAD recovers 95% of DOCK virtual actives for both targets after evaluating only 10% of the libraries. In breadth, RAD shows widespread applicability against 43 DUDE-Z proteins, evaluating 50.3 million associations. On average, RAD recovers 87% of virtual actives while docking 10% of the library without sacrificing chemical diversity

NASA Docking System Block 1: NASA's New Direct Electric Docking System Supporting ISS and Future Human Space Exploration

The NASA Docking System (NDS) Block 1 is a key component of NASA's vision for space exploration. It is designed to provide capability for visiting vehicles to dock to the International Space Station's recently-installed International Docking Adapter ports. It is the first docking system to be developed by NASA since the Apollo-Soyuz Test Project of the 1970's. The NDS Block 1 includes provisions for capture, structural attachment, power/data transfer, and undocking. It uses a direct-drive electromechanical Stewart Platform capture system architecture, along with an innovative automated control scheme, to achieve an unprecedented level of performance and simplicity. Its design implements the new International Docking System Standard, which will be a key enabler of diverse and flexible exploration missions in future iterations. NDS qualification was completed in 2017 to support a planned first flight in 2018 on the Boeing CST-100 Starliner

Design, synthesis and evaluation of praziquantel analogues and new molecular hybrids as potential antimalarial and anti-schistosomal agents

Malaria and schistosomiasis are two of the neglected tropical diseases that persistently wreak havoc worldwide. Although many antimalarial drugs such as chloroquine are readily available, the emergence of drug resistance necessitates the development of new therapies to combat this disease. Conversely, Praziquantel (PZQ) remains the sole effective drug against schistosomiasis, but its extensive use raises concerns about the potential for drug resistance to develop. In this project, the concept of molecular hybridization was used as a strategy to design the synthesis of new molecular hybrids with potential antimalarial and antischistosomal activity. A total of seventeen molecular hybrids and two PZQ analogues were prepared by coupling 6-alkylpraziquanamines with cinnamic acids and cyclohexane carboxylic acid, respectively. The synthesised compounds were evaluated for their antimalarial and antischistosomal activity; while all of the above compounds were inactive against Plasmodium falciparum (IC(50) > 6 µM), many were active against schistosomiasis with four particular compounds exhibiting up to 100% activity against newly transformed schistosomula and adult worms at 50 µM. Compared to PZQ, the reference drug, the activity of which is 91.7% at 1 µM, one particular molecular hybrid, compound 32, which bears a para-isopropyl group on the cinnamic acid moiety, exhibited a notable activity at 10 µM (78.2% activity). This compound has emerged as the front runner candidate that might, after further optimization, hold promise as a potential lead compound in the fight against schistosomiasis

Green fluorescent diamidines as diagnostic probes for trypanosomes

LED fluorescence microscopy offers potential benefits to the diagnosis of human African trypanosomiasis, as well as to other aspects of diseases management, such as detection of drug resistant strains. To advance such approaches reliable and specific fluorescent markers to stain parasites in human fluids are needed. Here we report a series of novel green fluorescent diamidines and their suitability as probes to stain trypanosomes

Electrostatic Patch Effect in Cylindrical Geometry. I. Potential and Energy between Slightly Non-Coaxial Cylinders

We study the effect of any uneven voltage distribution on two close cylindrical conductors with parallel axes that are slightly shifted in the radial and by any length in the axial direction. The investigation is especially motivated by certain precision measurements, such as the Satellite Test of the Equivalence Principle (STEP). By energy conservation, the force can be found as the energy gradient in the vector of the shift, which requires determining potential distribution and energy in the gap. The boundary value problem for the potential is solved, and energy is thus found to the second order in the small transverse shift, and to lowest order in the gap to cylinder radius ratio. The energy consists of three parts: the usual capacitor part due to the uniform potential difference, the one coming from the interaction between the voltage patches and the uniform voltage difference, and the energy of patch interaction, entirely independent of the uniform voltage. Patch effect forces and torques in the cylindrical configuration are derived and analyzed in the next two parts of this work.Comment: 26 pages, 1 Figure. Submitted to Classical and Quantum Gravit