Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 649 records · Page 36Linked to original sources

bioRxiv2024

Genetic purging of strongly deleterious mutations underlies black-necked crane's unusual escape from an extinction vortex

Many species are undergoing rapid demographic declines, necessitating an examination of the resulting genetic impacts. The prevailing small population paradigm posits an elevated genetic load and extinction risk. However, instances of fast recovery from severe population bottlenecks suggest alternative outcomes. To investigate this issue, we performed a population genomic analysis on the black-necked crane, analyzing 42 modern and 11 historical genomes. This study revealed substantial evidence of large-effect allele purging underlying the unexpectedly rapid population recovery following an abrupt bottleneck during the 1980s. Nevertheless, forward simulations supposing a prolonged bottleneck (e.g., five generations) predicted a reversion with negative prospects, implying that rapid population recovery served as both the cause and consequence of the species escaping from an extinction vortex. These findings shed light on a potential positive microevolutionary response to current widespread population collapses and underscore the urgency of implementing active and effective conservation strategies to reverse this trend before it becomes irreversible.

evolutionary biology↗

bioRxiv2024

Regional Glymphatic Dysfunction is linked to Spinocerebellar Ataxia Type 3 pathophysiology

Spinocerebellar ataxia type 3 (SCA3) involves neuroinflammation and imbalance between production and clearance of proteins which affects the glymphatic system, the lymphatic-like, fluid-transport system in the brain. However, it is unclear whether SCA3 is related to impairments in glymphatic function. Using multimodal imaging data, 34 SCA3 patients and 36 age-, sex- and educational matched healthy controls (HCs) were compared using multiple glymphatic measurements, including choroid plexus (CP) and cerebrospinal fluid (CSF) volume, diffusion tensor imaging along the perivascular (DTI-ALPS) index, and coupling relationship between blood-oxygen-level-dependent signals and CSF flow (BOLD-CSF coupling). Then, we evaluated regional glymphatic function by dividing DTI-ALPS and BOLD-CSF coupling into anterior, middle, posterior, and cerebellum regions, thereby identifying the spatial variation of glymphatic function in the two groups. We demonstrated that compared with HCs, larger CP and CSF volumes were found in SCA3 patients. More importantly, for DTI-ALPS index and BOLD-CSF coupling, these surrogate markers for glymphatic clearance were weaker in SCA3 patients. Furthermore, altered regional glymphatic functions were most prominent in midbrain, cerebellum and middle regions. Crucially, the altered midbrain, cerebellum, middle and global glymphatic functions were accompanied by the severity of ataxia and other SCA3 symptoms. Similar to other neurodegenerative disorders, the association between multiple glymphatic indexes and SCA3 symptoms suggested that waste clearance is disrupted in SCA3 patients, which shed light on the pathogenesis of this disease from a glymphatic lens. Our findings highlighted the dysregulated glymphatic function as a novel diagnostic marker for SCA3.

neuroscience↗

bioRxiv2024

Modeling of HIV-1 prophylactic efficacy and toxicity with islatravir shows non-superiority for oral dosing, but promise as a subdermal implant

HIV prevention with pre-exposure prophylaxis (PrEP) constitutes a major pillar in fighting the ongoing epidemic. While daily oral PrEP adherence may be challenging, long-acting (LA-)PrEP in oral or implant formulations could overcome frequent dosing with convenient administration. The novel drug islatravir (ISL) may be suitable for LA-PrEP, but high doses have been associated with lymphopenia. We developed a mathematical model to predict ISL pro-drug levels in plasma and active intracellular ISL-triphosphate concentrations after oral vs. subdermal implant dosing. Using phase-II trial data, we simulated antiviral effects and estimated HIV risk reduction for multiple dosages and dosing frequencies. We then established non-toxic exposure thresholds and evaluated low-dose regimens. Our findings suggest that implants with 56-62 mg ISL offer safe, effective HIV risk reduction without being toxic. Oral 0.1 mg daily, 3-5 mg weekly, and 10 mg bi-weekly ISL provide comparable efficacy, but weekly and bi-weekly doses resulted in residual toxicity, while adherence requirements for daily dosing were similar to established oral PrEP regimen. Oral 0.5-1 mg on-demand provided > 90% protection, while not being suitable for post-exposure prophylaxis.

systems biology↗

bioRxiv2024

A New Large-Scale Extracellular Vesicle Production Strategy for Biomedical Drug Development

1.Extracellular Vesicles (EVs) are nanoscale to microscale membranous vesicles released by cells. They are vital for intercellular communications in physiological and pathological conditions, offering immense potential in diagnostics and therapeutical applications due to their ability to transfer diverse biological cargos between cells. While research of EVs is continuously gaining popularity in academia, large-scale manufacturing aiming for clinical applications remains challenging. Herein, we introduce a novel large-scale EV production strategy, including an upstream process with fed-batch suspension HEK293 cell culture, and a downstream process with chromatographic purification for ultra-pure EVs. Such promising EV production strategy enables the potential capability of large scale GMP manufacture of EVs for clinical applications.

bioengineering↗

bioRxiv2024

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

Acute respiratory viral infections (ARVI), such as pneumovirus and respiratory picornavirus infections, exacerbate disease in COPD and asthma patients. A research program targeting respiratory syncytial virus (RSV) led to the discovery of GS-7682 (1) a novel phosphoramidate prodrug of a 4'-CN-4-aza-7,9-dideazaadenosine C-nucleoside GS-646089 (2) with broad antiviral activity against RSV EC50 = 3-46 nM, human metapneumovirus (hMPV) EC50 = 210 {+/-} 50 nM, human rhinovirus (RV) EC50 = 54-61 nM, and enterovirus (EV) EC50 = 83-90 nM. Prodrug optimization for cellular potency and lung cell metabolism identified the 5-methyl((S)-hydroxy(phenoxy)phosphoryl)-L-alaninate in combination with 2,3-diisobutyrate promoieties as optimal for high intracellular triphosphate formation in vitro and in vivo. 1 demonstrated significant reductions of viral loads in the lower respiratory tract of RSV-infected African green monkeys when administered once daily via intratracheal nebulized aerosol. Together these finding support additional evaluation of 1 and its analogs as a potential therapeutic for pneumo- and picornaviruses.

biochemistry↗

bioRxiv2024

ACE2-independent sarbecovirus cell entry is supported by TMPRSS2-related enzymes and reduces sensitivity to antibody-mediated neutralization

The COVID-19 pandemic, caused by SARS-CoV-2, demonstrated that zoonotic transmission of animal sarbecoviruses threatens human health but the determinants of transmission are incompletely understood. Here, we show that most spike (S) proteins of horseshoe bat and Malayan pangolin sarbecoviruses employ ACE2 for entry, with human and raccoon dog ACE2 exhibiting broad receptor activity. The insertion of a multibasic cleavage site into the S proteins increased entry into human lung cells driven by most S proteins tested, suggesting that acquisition of a multibasic cleavage site might increase infectivity of diverse animal sarbecoviruses for the human respiratory tract. In contrast, two bat sarbecovirus S proteins drove cell entry in an ACE2-independent, trypsin-dependent fashion and several ACE2-dependent S proteins could switch to the ACE2-independent entry pathway when exposed to trypsin. Several TMPRSS2-related cellular proteases but not the insertion of a multibasic cleavage site into the S protein allowed for ACE2-independent entry in the absence of trypsin and may support viral spread in the respiratory tract. Finally, the pan-sarbecovirus antibody S2H97 enhanced cell entry driven by two S proteins and this effect was reversed by trypsin. Similarly, plasma from quadruple vaccinated individuals neutralized entry driven by all S proteins studied, and use of the ACE2-independent, trypsin-dependent pathway reduced neutralization sensitivity. In sum, our study reports a pathway for entry into human cells that is ACE2-independent, supported by TMPRSS2-related proteases and associated with antibody evasion.

molecular biology↗

bioRxiv2024

The transcripts of a gastrula-premarked enhancer prime posterior tissue development through cross-talk with morphogen effector

The regulatory mechanisms governing cell fate determination, particularly lineage diversification during mammalian embryonic development, remain poorly understood with in-depth regulatory paradigms yet to be fully elucidated. Here, leveraging the epigenetic landscape of mouse gastrula, we identified p-Enh, a pre-marked enhancer in primitive streak region, as pivotal regulator for posterior tissue development in mouse embryos. Morphological and single-cell transcriptomic analyses confirmed embryonic lethality phenotype with disrupted posterior tissue development trajectories in p-Enh-KO embryos. Molecularly, apart from regulating the neighboring coding-gene Cdx2 in cis, our findings suggest that p-Enh also modulate the global transcriptome and epigenomic landscape, which might through the transient production of eRNA in trans. Further investigation revealed p-Enh participate in the regulatory cascades of TGF-{beta} signaling. Chemical modulation of TGF-{beta} signaling can largely rescue the posterior development deficiency in in vitro gastruloids through a Cdx2-independent mechanism. Thus, we propose a potential model in which the broadly distributed p-Enh transcripts within the nucleus could serve as essential cross-modular coordinators, priming the posterior development of mouse embryo.

developmental biology↗

bioRxiv2024

Directed evolution-based discovery of ligands for in vivo restimulation of CAR-T cells

Chimeric antigen receptor (CAR) T cell therapy targeting CD19 elicits remarkable clinical efficacy in B-cell malignancies, but many patients relapse due to failed expansion and/or progressive loss of CAR-T cells. We recently reported a strategy to potently restimulate CAR-T cells in vivo, enhancing their functionality by administration of a vaccine-like stimulus comprised of surrogate peptide ligands for a CAR linked to a lymph node-targeting amphiphilic PEG-lipid (termed CAR-T-vax). Here, we demonstrate a general strategy to generate and optimize peptide mimotopes enabling CAR-T-vax generation for any CAR. Using the clinical CD19 CAR (FMC63) as a test case, we employed yeast surface display to identify peptide binders to soluble IgG versions of FMC63, which were subsequently affinity matured by directed evolution. CAR-T vaccines using these optimized mimotopes triggered marked expansion and memory development of CD19 CAR-T cells in both syngeneic and humanized mouse models of B-ALL/Lymphoma, and enhanced control of disease progression. This approach thus enables vaccine boosting to be applied to any clinically relevant CAR-T cell product.

bioengineering↗

bioRxiv2024

Mutations in the IgG B cell receptor associated with class-switched B cell lymphomas

Immunoglobulin class-switching from IgM to IgG enhances B cell receptor (BCR) signalling1,2 and promotes germinal centre (GC) B cell responses to antigens3,4. In contrast, non-Hodgkin lymphomas derived from GC B cells typically avoid IgG BCR expression and retain the unswitched IgM BCR, suggesting that the IgG BCR may protect B cells from malignant transformation5,6. However, the mechanism of this phenomenon and its significance for the pathogenicity of IgG-expressing lymphomas remains unclear. Here, we report that IgG-positive follicular lymphoma (FL) and the related EZB subset of diffuse large B cell lymphoma (DLBCL) acquire mutations in the IgG heavy chain, disrupting its unique intracellular tail. Enforced class switching of IgM-expressing EZB DLBCL cell lines to IgG reduces BCR surface levels, signalling via phosphoinositide-3 kinase (PI3K), levels of MYC, cell proliferation and in vivo growth. Inhibiting GSK3, a target of BCR-PI3K signalling, or stimulating the BCR rescues IgG+ cell proliferation. In contrast, IgG tail-truncating mutations enhance BCR surface expression, intracellular signalling and competitive growth. These findings suggest that the expansion of IgG-switched GC-like B lymphoma cells is limited by low tonic PI3K activity of the wild-type IgG BCR, but a subset of these cancers acquires mutations of the IgG intracellular tail that reverse this effect, promoting the oncogenicity of their BCRs. The presence of IgG tail mutations underscores the importance of isotype-specific BCR signalling in the pathogenesis of FL and EZB DLBCL and can potentially inform therapeutic targeting with BCR signalling inhibitors or antibody-drug conjugates.

immunology↗

bioRxiv2024

Comparative genomics of macaques and integrated insights into genetic variation and population history

The crab-eating macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is [~]42% lower, while centromeres are [~]3.7 times longer than those in humans. The characterization of [~]2 Mbp fixed genetic variants and [~]240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1, SEMA3F, and HOXD13). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.

genomics↗

bioRxiv2024

Transcriptional activation of Bmal1 drives the inflammatory activity of monocytes by modulating mitochondrial unfolded protein response during hypobaric hypoxic stress

BackgroundHypoxic stress-induced inflammation had been considered to play an important role in the onset and progression of altitude-related illnesses, but the origin of inflammatory cytokines, the specific responding cell types, and molecular mechanisms remain unknown. Mitochondria are responsible for oxygen consumption and recently reported to be the master regulators of inflammation, but it is not clear whether and how mitochondrial organelles sense the hypoxic stress and then control the inflammation. MethodsHuman subjects and mouse models were exposed to real or simulated altitude of 5500 m. Bone marrow-derived macrophages (BMDMs) and monocyte RAW264.7 cells were cultured under 1% oxygen hypoxic conditions. Myeloid-specific Bmal1 knock-out mice were generated by crossing Bmal1flox/flox mice with Lyz2-Cre mice. Inflammation was investigated by assessing inflammatory mediators, monocyte activities, and leukocyte infiltrating. Mitochondrial unfolded protein response was examined by measuring stress markers, such as LONP1, AFG3L2, and HSP60. The target molecular mechanisms were identified by performing bioinformatic analyses, ChIP assays, and gain/loss-of-function experiments. Results1) Monocytes in peripheral blood mononuclear cell (PBMCs) were more sensitive and contributed promptly to circulating inflammation in response to acute hypobaric hypoxia. 2) Hypoxic stress triggered the mitochondrial unfolded protein response and then induced the mito-inflammation (NLRP3 inflammasome) in monocytes. 3) Activation of Bmal1 drove mitochondrial stress and mito-inflammation by promoting Fis1-mediated mitochondrial fission in monocytes under hypoxia. 4) BHLHE40, a stress-responsive transcription factor directly targeted by HIF-1, stimulated Bmal1 transcription in monocytes under hypobaric hypoxia. 5) Myeloid-specific Bmal1 deletion alleviated systemic circulating and vascular inflammation under acute hypobaric hypoxia. ConclusionBHLHE40, a transcription factor associated with hypoxia, stimulated Bmal1, which in turn triggered the mitochondrial unfolded protein response and drove the mito-inflammation in monocytes by promoting Fis1-mediated mitochondrial fission. Our work provides a novel mechanism which may develop the circadian targeting drugs for altitude or hypoxia-related diseases.

molecular biology↗

bioRxiv2024

The subcommissural organ regulates brain development via secreted peptides

The subcommissural organ (SCO) is a gland located at the entrance of the aqueduct of Sylvius in the brain. It exists in species as distantly related as amphioxus and humans, but its function is largely unknown. To explore its function, we compared transcriptomes of SCO and non-SCO brain regions and found three genes, Sspo, Car3, and Spdef, that are highly expressed in the SCO. Mouse strains expressing Cre recombinase from endogenous promoter/enhancer elements of these genes were used to genetically ablate SCO cells during embryonic development, resulting in severe hydrocephalus and defects in neuronal migration and development of neuronal axons and dendrites. Unbiased peptidomic analysis revealed enrichment of three SCO-derived peptides, namely thymosin beta 4, thymosin beta 10, and NP24, and their reintroduction into SCO-ablated brain ventricles substantially rescued developmental defects. Together, these data identify a critical role for the SCO in brain development.

neuroscience↗

bioRxiv2024

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism

Nematode-trapping fungi (NTF), most of which belong to a monophyletic lineage in Ascomycota, cannibalize nematodes and other microscopic animals, raising questions regarding the types and mechanisms of genomic changes that enabled carnivorism and adaptation to the carbon-rich and nitrogen-poor environment created by the Permian-Triassic extinction event. Here, we conducted comparative genomic analyses of 21 NTF and 21 non-NTF to address these questions. Carnivorism-associated changes include expanded genes for nematode capture, infection, and consumption (e.g., adhesive proteins, CAP superfamily, eukaryotic aspartyl proteases, and serine-type peptidases). Although the link between secondary metabolite (SM) production and carnivorism remains unclear, we found that the numbers of SM gene clusters among NTF are significantly lower than those among non-NTF. Significantly expanded cellulose degradation gene families (GH5, GH7, AA9, and CBM1) and contracted genes for carbon-nitrogen hydrolases (enzymes that degrade organic nitrogen to ammonia) are likely associated with adaptation to the carbon-rich and nitrogen-poor environment. Through horizontal gene transfer events from bacteria, NTF acquired the Mur gene cluster (participating in synthesizing peptidoglycan of the bacterial cell wall) and Hyl (a virulence factor in animals). Disruption of MurE reduced NTFs ability to attract nematodes, supporting its role in carnivorism. This study provides new insights into how NTF evolved and diversified after the Permian-Triassic mass extinction event.

evolutionary biology↗

bioRxiv2024

Altruistic feeding and cell-cell signaling during bacterial differentiation actively enhance phenotypic heterogeneity

Starvation triggers bacterial spore formation, a committed differentiation program that transforms a vegetative cell into a dormant spore. Cells in a population enter sporulation non-uniformly to secure against the possibility that favorable growth conditions, which puts sporulation-committed cells at a disadvantage, may resume. This heterogeneous behavior is initiated by a passive mechanism: stochastic activation of a master transcriptional regulator. Here, we identify a cell-cell communication pathway that actively promotes phenotypic heterogeneity, wherein Bacillus subtilis cells that start sporulating early utilize a calcineurin-like phosphoesterase to release glycerol, which simultaneously acts as a signaling molecule and a nutrient to delay non-sporulating cells from entering sporulation. This produced a more diverse population that was better poised to exploit a sudden influx of nutrients compared to those generating heterogeneity via stochastic gene expression alone. Although conflict systems are prevalent among microbes, genetically encoded cooperative behavior in unicellular organisms can evidently also boost inclusive fitness.

microbiology↗

bioRxiv2024

A candidate reference method for the quantification of α-synuclein in cerebrospinal fluid using an SI traceable primary calibrator and multiple reaction monitoring

Objectives-synuclein aggregation is an indicator of neurodegenerative diseases such as Parkinsons disease (PD) and recent advances have suggested that this protein could serve as a potential biomarker. It has been indicated that soluble and oligomeric -synuclein in biological fluids could have diagnostic applications for PD. Clinical laboratories currently rely on antibody-based assays to detect -synuclein. These assays have limited specificity, low sensitivity and poor inter-lab reproducibility, which prevents the validation of -synuclein as a biomarkers. This study aims to fill the unmet need for the standardisation of clinical measurements for -synuclein. MethodsWe report the first candidate reference method for -synuclein, using an SI traceable primary calibrator for -synuclein and isotope dilution mass spectrometry. The primary calibrator was traceably quantified utilising a combination of amino acid analysis and nuclear magnetic resonance. A targeted sample clean-up procedure involving a non-denaturing Lys-C digestion and solid-phase extraction allowed for the sensitive detection of multiple proteotypic -synuclein peptides in cerebrospinal fluid (CSF) samples. ResultsThe candidate reference method procedure showed linearity across three orders of magnitude, covering the physiological levels of -synuclein in CSF (LOQ = 0.1 ng/g). The method was used to quantify a cohort of CSF samples and the measurements were correlated with immunoassay-based quantifications. ConclusionsThe SI traceable quantification of -synuclein in complex biological matrices means that the role of this protein can be further elucidated in synucleinopathies. This candidate reference method would lead to the harmonisation of -synuclein measurements, which may allow for development of high throughput clinical tests.

biochemistry↗

bioRxiv2024

Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase in prokaryotes

Protein N--lysine acetylation (Kac) modifications play crucial roles in diverse physiological and pathological functions in cells. In prokaryotic cells, there are only two types of lysine deacetylases (KDACs) that are Zn2+- or NAD+-dependent. In this study, we reported a protein, AhCobQ, in Aeromonas hydrophila ATCC 7966 that presents NAD+- and Zn2+-independent KDAC activity. Furthermore, its KDAC activity is located in an unidentified domain (from 195-245 aa). Interestingly, AhCobQ has no homology with current known KDACs, and no homologous protein was found in eukaryotic cells. A protein substrate analysis showed that AhCobQ has specific protein substrates in common with other known KDACs, indicating that these KDACs can dynamically co-regulate the states of Kac proteins. Microbiological methods employed in this study affirmed AhCobQs positive regulation of isocitrate dehydrogenase (ICD) enzymatic activity at the K388 site, implicating AhCobQ in the modulation of bacterial enzymatic activities. In summary, our findings present compelling evidence that AhCobQ represents a distinctive type of KDAC with significant roles in bacterial biological functions. SummaryThe lack of exploration of new lysine acetylases and deacetylases (KDACs) and their protein substrates in prokaryotic cells has become a bottleneck in the functional study of lysine acetylation modifications. In this study, we reported a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila. Interestingly, this protein does not share homology with current known KDACs, and its KDAC activity is located in an unknown domain for which a homologous protein cannot be found in eukaryotic cells. The following analysis showed that AhCobQ affected the enzymatic activity and protein-protein interaction ability of its protein substrates. In summary, these results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications. HighlightsAhCobQ is an NAD+- and Zn2+-independent protein lysine deacetylase. There are no proteins homologous to AhCobQ in eukaryotes. The deacetylase activity of AhCobQ is located in an unknown domain. AhCobQ has specific protein substrates and substrates in common with other lysine deacetylases. AhCobQ positively regulates the enzymatic activity of isocitrate dehydrogenase at its K388 site.

microbiology↗

bioRxiv2024

SARS-CoV-2 infection activates inflammatory macrophages in vascular immune organoids

SARS-CoV-2 provokes devastating tissue damage by cytokine release syndrome and leads to multi-organ failure. Modeling the process of immune cell activation and subsequent tissue damage is a significant task. Organoids from human tissues advanced our understanding of SARS-CoV-2 infection mechanisms though, they are missing crucial components: immune cells and endothelial cells. This study aims to generate organoids with these components. We established vascular immune organoids from human pluripotent stem cells and examined the effect of SARS-CoV-2 infection. We demonstrated that infections activated inflammatory macrophages. Notably, the upregulation of interferon signaling supports macrophages role in cytokine release syndrome. We propose vascular immune organoids are a useful platform to model and discover factors that ameliorate SARS-CoV-2-mediated cytokine release syndrome.

immunology↗

bioRxiv2024

CLigOpt: Controllable Ligand Design through Target-Specific Optimisation

AO_SCPCAPBSTRACTC_SCPCAPO_ST_ABSMotivationC_ST_ABSKey challenge in deep generative models for molecular design is to navigate random sampling of the vast molecular space, and produce promising molecules that compromise property controls across multiple chemical criteria. Fragment-based drug design (FBDD), using fragments as starting points, is an effective way to constrain chemical space and improve generation of biologically active molecules. Furthermore, optimisation approaches are often implemented with generative models to search through chemical space, and identify promising samples which satisfy specific properties. Controllable FBDD has promising potential in efficient target-specific ligand design. ResultsWe propose a controllable FBDD model, CLigOpt, which can generate molecules with desired properties from a given fragment pair. CLigOpt is a Variational AutoEncoder-based model which utilises co-embeddings of node and edge features to fully mine information from molecular graphs, as well as a multi-objective Controllable Generation Module to generate molecules under property controls. CLigOpt achieves consistently strong performance in generating structurally and chemically valid molecules, as evaluated across six metrics. Applicability is illustrated through ligand candidates for hDHFR and it is shown that the proportion of feasible active molecules from the generated set is increased by 10%. Molecular docking and synthesisability prediction tasks are conducted to prioritise generated molecules to derive potential lead compounds. Availability and ImplementationThe source code is available via https://github.com/yutongLi1997/CLigOpt-Controllable-Ligand-Design-through-Target-Specific-Optimisation.

bioinformatics↗