Nigam, A. | bioRxiv Science

bioRxiv2023

VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules

Identifying potent lead molecules for specific targets remains a major bottleneck in drug discovery. As structural information about proteins becomes increasingly available, ultra-large virtual screenings (ULVSs) which computationally evaluate billions of molecules offer a powerful way to accelerate early-stage drug discovery. Here, we introduce AdaptiveFlow, an open-source platform designed to make ULVSs more accessible, scalable, and efficient. AdaptiveFlow provides free access to a screening-ready version of the Enamine REAL Space (1), the largest library of ready-to-dock, drug-like molecules, containing 69 billion compounds that we prepared using the ligand preparation module of the platform. A key innovation of the platform is its use of a multi-dimensional grid of molecular properties, which helps researchers explore and prioritize chemical space more effectively and reduce the computational costs by a factor of approximately 1000. This grid forms the basis of a new method for identifying promising regions of chemical space, enabling systematic exploration and prioritization of compound libraries. An optional active learning component can further accelerate this process by adaptively steering the search toward molecules most likely to bind a given target. To support a broad range of applications, AdaptiveFlow is compatible with over 1,500 docking protocols. The platform achieves near-linear scaling on up to 5.6 million CPUs in the AWS Cloud, setting a new benchmark for large-scale cloud computing in drug discovery. Using this approach, we identified nanomolar inhibitors of two disease-relevant targets: ferroptosis suppressor protein 1 (FSP1) and poly(ADP-ribose) polymerase 1 (PARP-1) (2, 3). By leveraging newly solved crystal structures of FSP1 in complex with NAD+, FAD, and coenzyme Q1, we validated these hits experimentally and determined the co-crystal structures of FSP1 bound to small-molecule inhibitors, enabling insights into inhibitor binding mechanisms previously unknown. With its high scalability, flexibility, and open accessibility, AdaptiveFlow offers a powerful new resource for discovering and optimizing drug candidates at an unprecedented scale and speed.

bioinformatics↗

bioRxiv2021

mTOR-activating mutations in RRAGD cause kidney tubulopathy and cardiomyopathy (KICA) syndrome

BackgroundOver the last decaces, advances in genetic techniques have resulted in the identification of rare hereditary disorders of renal magnesium and salt handling. Nevertheless, {+/-}20% of all tubulopathy patients remain without genetic diagnosis. Here, we explore a large multicentric patient cohort with a novel inherited salt-losing tubulopathy, hypomagnesemia and dilated cardiomyopathy (DCM). MethodsWhole exome and genome sequencings were performed with various subsequent functional analyses of identified RRAGD variants in vitro. ResultsIn 8 children from unrelated families with a tubulopathy characterized by hypomagnesemia, hypokalemia, salt-wasting, and nephrocalcinosis, we identified heterozygous missense variants in RRAGD that mostly occurred de novo. Six of these patients additionally suffered from DCM requiring heart transplantation in 3 of them. An additional dominant variant in RRAGD was simultaneously identified in eight members of a large family with a similar renal phenotype. RRAGD encodes GTPase RagD mediating amino acid signaling to the mechanistic target of rapamycin complex 1 (mTORC1). RagD expression along the mammalian nephron include the thick ascending limb and the distal convoluted tubule. The identified RRAGD variants were shown to induce a constitutive activation of mTOR signaling in vitro, ConclusionsOur findings establish a novel disease phenotype combining kidney tubulopathy and cardiomyopathy (KICA) caused by an activation of mTOR signaling suggesting a critical role of Rag GTPase D for renal electrolyte handling and cardiac function. SIGNIFICANCE STATEMENTHere, we report on heterozygous variants in RRAGD in patients with profound hypomagnesemia, renal salt wasting, nephrocalcinosis, and dilated cardiomyopathy. The identified RagD variants induce a constitutive activation of mTOR signaling in vitro. These findings not only establish a novel monogenic disorder of the kidney tubule, but demonstrate the essential role of mTOR signaling for distal tubular electrolyte handling and cardiac function.

genetics↗