Regression-Based Active Learning for Accessible Acceleration of Ultra-Large Library Docking

Structure-based drug discovery is a process for both hit finding and optimization that relies on a validated three-dimensional model of a target biomolecule, used to rationalize the structure-function relationship for this particular target. An ultralarge virtual screening approach has emerged recently for rapid discovery of high-affinity hit compounds, but it requires substantial computational resources. This study shows that active learning with simple linear regression models can accelerate virtual screening, retrieving up to 90% of the top-1% of the docking hit list after docking just 10% of the ligands. The results demonstrate that it is unnecessary to use complex models, such as deep learning approaches, to predict the imprecise results of ligand docking with a low sampling depth. Furthermore, we explore active learning meta-parameters and find that constant batch size models with a simple ensembling method provide the best ligand retrieval rate. Finally, our approach is validated on the ultralarge size virtual screening data set, retrieving 70% of the top-0.05% of ligands after screening only 2% of the library. Altogether, this work provides a computationally accessible approach for accelerated virtual screening that can serve as a blueprint for the future design of low-compute agents for exploration of the chemical space via large-scale accelerated docking. With recent breakthroughs in protein structure prediction, this method can significantly increase accessibility for the academic community and aid in the rapid discovery of high-affinity hit compounds for various targets.

Evaluation of variable new antigen receptors (vNARs) as a novel cathepsin S (CTSS) targeting strategy

Aberrant activity of the cysteine protease Cathepsin S (CTSS) has been implicated across a wide range of pathologies. Notably in cancer, CTSS has been shown to promote tumour progression, primarily through facilitating invasion and migration of tumour cells and augmenting angiogenesis. Whilst an attractive therapeutic target, more efficacious CTSS inhibitors are required. Here, we investigated the potential application of Variable New Antigen Receptors (vNARs) as a novel inhibitory strategy. A panel of potential vNAR binders were identified following a phage display panning process against human recombinant proCTSS. These were subsequently expressed, purified and binding affinity confirmed by ELISA and SPR based approaches. Selected lead clones were taken forward and were shown to inhibit CTSS activity in recombinant enzyme activity assays. Further assessment demonstrated that our lead clones functioned by a novel inhibitory mechanism, by preventing the activation of proCTSS to the mature enzyme. Moreover, using an intrabody approach, we exhibited the ability to express these clones intracellularly and inhibit CTSS activity whilst lead clones were also noted to impede cell invasion in a tumour cell invasion assay. Collectively, these findings illustrate a novel mechanistic approach for inhibiting CTSS activity, with anti-CTSS vNAR clones possessing therapeutic potential in combating deleterious CTSS activity. Furthermore, this study exemplifies the potential of vNARs in targeting intracellular proteins, opening a range of previously "undruggable" targets for biologic-based therapy.

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P_1-5. S1P₅ is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P₅ receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P₅-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family.

S1P₅ is a sphingosine-1-phosphate (S1P) receptor implicated in immune and neurodegenerative disorders. Here, authors report a crystal structure of the S1P₅ receptor in complex with a selective inverse agonist, revealing an allosteric subpocket and shedding light on inverse agonism in S1P receptors.

Nonstationary dynamics of the sine lattice consisting of three pendula (trimer)

The low- and high-amplitude oscillations in the system of three nonlinear coupled pendula (trimer) are analyzed beyond the quasilinear approximation. The considered oscillations are fundamental for many models of the energy exchange processes in physical, mechanical, and biological systems, in particular, for the torsional vibrations of flexible polymers or DNA's double strands. We obtained the conditions of the basic stationary solutions' stability. These solutions correspond to the nonlinear normal modes (NNMs), the instability of which leads to the appearance of localized NNMs (stationary energy localization). Using an asymptotic procedure, we reduce the dimension of the system's phase space that allows us to analyze the energy exchange between pendula in the slow timescale and to reveal periodic interparticle energy exchange and nonstationary energy localization. It has been shown recently that essentially nonstationary resonance processes of this type are adequately described in terms of the limiting phase trajectories (LPTs) corresponding to beatings between the oscillators or coherence domains in the slow timescale. Moreover, it turns out that criteria of the transition to the stationary and nonstationary energy localization can be formulated as the bifurcation conditions for NNMs and LPTs, respectively. The trimer under consideration is a nonintegrable system, and therefore its equations of motion is only after dimensions reduction can be analyzed by the Poincare sections method. Finally, we aim to study the highly nonstationary regimes, which correspond to beatinglike periodic or quasiperiodic recurrent energy exchange between the pendula.

Emergence of non-stationary regimes in one- and two-dimensional models with internal rotators

In the present paper, we give a selective review of some very recent works concerning the non-stationary regimes emerging in various one- and two-dimensional models incorporating internal rotators. In one-dimensional models, these regimes are characterized by the intense energy transfer from the outer element, subjected to initial or harmonic excitation, to the internal rotator. As for the two-dimensional models (incorporating internal rotators), we will mainly focus on the two special dynamical states, namely a state of the near-complete energy transfer from longitudinal to lateral vibrations of the outer element as well as the state of a permanent, unidirectional energy locking with mild, spatial energy exchanges. In this review, we will discuss the recent theoretical and experimental advancements in the study of essentially nonlinear mechanisms governing the formation and bifurcations of the regimes of intense energy transfer. The present review is composed of two parts. The first part will be mainly devoted to the emergence of resonant energy transfer states in one-dimensional models incorporating internal rotators, while the second part will be mainly concerned with the manifestation of various energy transfer states in two-dimensional ones.This article is part of the theme issue 'Nonlinear energy transfer in dynamical and acoustical systems'.

Nonconventional synchronization and energy localization in weakly coupled autogenerators

The present work follows our previous study dealing with a new type of synchronization in a system of two weakly coupled generalized van der Pol-Duffing autogenerators. The essence of the effect revealed is that the synchronized oscillations are not stationary but accompanied by the most intensive energy exchange between the oscillators. The phase shift between the generators remains constant most of the time, except for vanishingly small transitional intervals. The current analysis deals with a generalized model in order to clarify the frequency detuning effect. We found that varying the frequency detuning, nonlinearity, and dissipation parameters can lead to structural changes in phase diagrams of the energy exchange dynamics, with important transitions from the intensive energy exchange to its localization on one of the two oscillators. The main conclusion is that stationary and nonstationary synchronizations associate with nonlinear normal and local modes, respectively. The analysis uses phase plane diagrams, including the concept of limiting phase trajectories, whose role in nonstationary synchronization appears to be similar to the role of nonlinear normal modes in conventional stationary states.

Consecutive transitions from localized to delocalized transport states in the anharmonic chain of three coupled oscillators

In the present paper, we study the mechanism of formation and bifurcations of highly nonstationary regimes manifested by different energy transport intensities, emerging in an anharmonic trimer model. The basic model under investigation comprises a chain of three coupled anharmonic oscillators subject to localized excitation, where the initial energy is imparted to the first oscillator only. We report the formation of three basic nonstationary transport states traversed by locally excited regimes. These states differ by spatial energy distribution, as well as by the intensity of energy transport along the chain. In the current study, we focus on numerical and analytical investigation of the intricate resonant mechanism governing the inter-state transitions of locally excited regimes. Results of the analytical study are in good agreement with the numerical simulations of the trimer model.