High-affinity Ligand Research Articles

High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.

Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.

Abstract 14054: Monocyte Vascular Endothelial Growth Factor Receptor-1 Signaling in Peripheral Artery Disease

Introduction: Peripheral artery disease (PAD) is caused by atherosclerosis of large arteries of the leg(s). Beyond complications from poor perfusion to the legs, patients with PAD suffer higher than expected rates of heart attack and strokes. Monocytes are subdivided into three subtypes: CD14++CD16- (classical), CD14+CD16+ (intermediate), and CD14-CD16+ (non-classical). The intermediate monocyte subtype is linked to PAD. Vascular Endothelial Growth Factor receptor (VEGFR)-1 is a member of tyrosine kinase family that is expressed in monocytes and has high affinity for the VEGF-A ligand. Recent studies showed that inhibition of VEGFR1/STAT-3 signaling decreases angiogenesis in PAD. We hypothesized that in patients with PAD, intermediate monocytes would have less VEGFR1/STAT3 activation than controls. Methods: Blood samples were collected from PAD patients (n=11) and risk factor closely matched controls (n=17). PBMCs were isolated by gradient centrifugation. By flow cytometry, gating strategy on monocytes was done by excluding granulocytes (CD66b), B and T lymphocytes (CD3,CD19), and natural killer cells (CD56). Next, monocytes were subdivided into three populations (intermediate, classical, and non-classical) by gating according to their CD14/CD16 expression. Within each population, levels of p(Y1333)VEGFR1, VEGFR1, pSTAT3, and STAT3 were determined. Results: Data from flow cytometry analysis showed a significant increase in the intermediate monocyte population in PAD vs control (~1.5-fold change; p=0.01). However, there was no significant difference in the non-classical or classical monocytes between PAD and control. Within the intermediate monocytes, P(Y1333) VEGFR1/VEGFR1 was decreased (~2-fold change) and pSTAT3/STAT3 was significantly decreased (~2-fold change) in PAD vs control. In both the non-classical and classical monocytes, there was no significant difference in either phosphorylated receptor between PAD and control. Conclusions: The data confirm the intermediate monocyte is associated with PAD and suggest that VEGFR1/STAT3 signaling is decreased in intermediate monocytes in PAD vs control. Understanding the mechanism of VEGFR1 activation may prove to be a promising therapeutic target for patients with PAD.

Evaluation of Pharmacological Rescue of Melanocortin-4 Receptor Nonsense Mutations by Aminoglycoside.

The melanocortin-4 receptor (MC4R) is critical for central satiety regulation, therefore presenting a potent target for pharmacological obesity treatment. Melanocortin-4 receptor mutations prevalently cause monogenetic obesity. A possibility of overcoming stop mutations is aminoglycoside-mediated translational readthrough. Promising results were achieved in COS-7 cells, but data for human cell systems are still missing, so uncertainty surrounds this potential treatment. In transfected HEK-293 cells, we tested whether translational readthrough by aminoglycoside Geneticin combined with high-affinity ligand setmelanotide, which is effective in proopiomelanocortin or leptin receptor deficiency patients, is a treatment option for affected patients. Five MC4R nonsense mutants (W16X, Y35X_D37V, E61X, W258X, Q307X) were investigated. Confocal microscopy and cell surface expression assays revealed the importance of the mutations' position within the MC4R. N-terminal mutants were marginally expressed independent of Geneticin treatment, whereas mutants with nonsense mutations in transmembrane helix 6 or helix 8 showed wild-type-like expression. For functional analysis, Gs and Gq/11 signaling were measured. N-terminal mutants (W16X, Y35X_D37V) showed no cAMP formation after challenge with alpha-MSH or setmelanotide, irrespective of Geneticin treatment. Similarly, Gs activation was almost impossible in W258X and Q307X with wild-type-like cell surface expression. Results for Gq/11 signaling were comparable. Based on our data, this approach improbably represents a therapeutic option.

Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor

The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, 1H-STD and 15N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.

Conjugates of adenosine mimetics and arginine-rich peptides serve as inhibitors and fluorescent probes but not as long-lifetime photoluminescent probes for protein arginine methyltransferases.

The conjugates of an adenosine mimetic and oligo-l-arginine or oligo-d-arginine (ARCs) were initially designed in our research group as inhibitors and photoluminescent probes targeting basophilic protein kinases. Here, we explored a panel of ARCs and their fluorescent derivatives in biochemical assays with members of the protein arginine methyltransferase (PRMT) family, focusing specifically on PRMT1. In the binding/displacement assay with detection of fluorescence anisotropy, we found that ARCs and arginine-rich peptides could serve as high-affinity ligands for PRMT1, whereas the equilibrium dissociation constant values depended dramatically on the number of arginine residues within the compounds. The fluorescently labeled probe ARC-1081 was displaced from its complex with PRMT1 by both S-adenosyl-l-methionine (SAM) and S-adenosyl-l-homocysteine (SAH), indicating binding of the adenosine mimetic of ARCs to the SAM/SAH-binding site within PRMT1. The ARCs that had previously shown microsecond-lifetime photoluminescence in complex with protein kinases did not feature such property in complex with PRMT1, demonstrating the selectivity of the time-resolved readout format. When tested against a panel of PRMT family members in single-dose inhibition experiments, a micromolar concentration of ARC-902 was required for the inhibition of PRMT1 and PRMT7. Overall, our results suggest that the compounds containing multiple arginine residues (including the well-known cell-penetrating peptides) are likely to inhibit PRMT and thus interfere with the epigenetic modification status in complex biological systems, which should be taken into consideration during interpretation of the experimental data.

Insertion of circularly permuted cyan fluorescent protein into the ligand-binding domain of inositol 1,4,5-trisphosphate receptor for enhanced FRET upon binding of fluorescent ligand

Binding of fluorescent ligand (FL) to the cyan fluorescent protein (CFP)-coupled ligand-binding domain of the inositol 1,4,5-trisphosphate (IP3) receptor (CFP-LBP) produces fluorescence (Förster) resonance energy transfer (FRET). A competitive fluorescent ligand assay (CFLA), using the FRET signal from competition between FLs and IP3, can measure IP3 concentration. The FRET signal should be enhanced by attaching a FRET donor to an appropriate position. Herein, we inserted five different circularly permuted CFPs in the loop between the second and third α-helices to generate membrane-targeted fluorescent ligand-binding proteins (LBPs). Two such proteins, LBP-cpC157 and LBP-cpC173, localized at the plasma membrane, displayed FRET upon binding the high-affinity ligand fluorescent adenophostin A (F-ADA), and exhibited a decreased fluorescence emission ratio (480 nm / 535 nm) by 1.6- to 1.8-fold that of CFP-LBP. In addition, binding of a fluorescent low-affinity ligand (F-LL) also reduced the fluorescence ratio in a concentration-dependent manner, with EC50 values for LBP-cpC157 and LBP-cpC173 of 34.7 nM and 27.6 nM, respectively. These values are comparable to that with CFP-LBP (29.2 nM), indicating that insertion of cpC157 and cpC173 did not disrupt LBP structure and function. The effect of 100 nM F-LL on the decrease in fluorescence ratio was reversed upon addition of IP3, indicating binding competition between F-LL and IP3. We also constructed cytoplasmic fluorescent proteins cyLBP-cpC157 and cyLBP-cpC173, and bound them to DYK beads for imaging analyses. Application of F-ADA decreased the fluorescence ratio of the beads from the periphery to the center over 3 − 5 min. Application of F-LL also decreased the fluorescence ratio of cyLBP-cpC157 and cyLBP-cpC173 by 20−25%, and subsequent addition of IP3 recovered the fluorescence ratio in a concentration-dependent manner. The EC50 value and Hill coefficient obtained by curve fitting against the IP3-dependent recovery of fluorescence ratio can be used to estimate the IP3 concentration.

PSMA1-mediated ultrasmall gold nanoparticles facilitate tumor targeting and MR/CT/NIRF multimodal detection of early-stage prostate cancer

Prostate-specific membrane antigen (PSMA) is a prominent biomarker for prostate cancer (PCa) diagnosis. Safe contrast agents able to render the expression and distribution of PSMA would facilitate early accurate screening and prognostic prediction of PCa. However, current Gd-containing nanoparticles are often limited by nonspecific redistribution in mononuclear phagocyte system (MPS) and inadequate perfusion to target sites. Besides, intrinsic defects of magnetic resonance (MR) equipment also hamper their use for precisely depicting PSMA details. Herein, we devised a novel noninvasive MR/CT/NIRF multimodal contrast agent (AGGP) coordinated to a high-affinity PSMA ligand (PSMA1) to specifically detect and quantify PSMA expression in PCa lesions, which exhibited formidable tripe-modal signal augments, preferential PSMA targeting, effective MPS escaping and profitable renal-clearable behavior in living mice. Biocompatibility and histopathological studies substantiated high security of AGGP in vivo, opening the door to future opportunities for improving early-stage PCa detection and clinical implementation of more effective multifunctional nanotherapeutics.

Hyaluronic acid-coated proglycosomes for topical delivery of tofacitinib in rheumatoid arthritis condition: Formulation design, in vitro, ex vivo characterization, and in vivo efficacy studies

Tofacitinib (TF) is a selective oral jakanib approved by the USFDA for the treatment of rheumatoid arthritis (RA). To overcome the adverse effects of orally administered TF, topical delivery can be a suitable choice. The therapeutic efficacy of TF can be improved through the high affinity of natural ligands (hyaluronic acid and chondroitin sulphate) to CD44 receptors on the macrophages or other immune cells in the dermal region. Thus, the present research work was inspired by the possibility to develop and evaluate the potential of hyaluronic acid-coated proglycosomes (HA-TF-PG) as the carrier for site-specific dermal delivery. The normal-PG (N-TF-PG) and HA-TF-PG showed particle sizes of <250 nm. The HA-TF-PG demonstrated 3.15-fold higher retention of TF in the viable dermis layers than the conventional formulation. The in vivo pharmacodynamic study, cytokines, and radiographic study on Complete Freud's Adjuvant-induced arthritic rat model revealed that HA-TF-PG exhibited a significant (P < 0.001) reduction in inflammation in arthritic rat's paw compared to the conventional TF. The developed HA-TF-PG treated groups showed significantly lowered CD44 levels compared to FD-gel and N-TF-PG i.e. 2.28 and 1.32-fold respectively (p < 0.001). In conclusion, The HA-TF-PG can be developed as an effective carrier for the site-specific dermal drug delivery system of TF to treat RA.

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site.

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

Discovery of N-β-l-Fucosyl Amides as High-Affinity Ligands for the Pseudomonas aeruginosa Lectin LecB.

The Gram-negative pathogen Pseudomonas aeruginosa causes severe infections mainly in immunocompromised or cystic fibrosis patients and is able to resist antimicrobial treatments. The extracellular lectin LecB plays a key role in bacterial adhesion to the host and biofilm formation. For the inhibition of LecB, we designed and synthesized a set of fucosyl amides, sulfonamides, and thiourea derivatives. Then, we analyzed their binding to LecB in competitive and direct binding assays. We identified β-fucosyl amides as unprecedented high-affinity ligands in the two-digit nanomolar range. X-ray crystallography of one α- and one β-anomer of N-fucosyl amides in complex with LecB revealed the interactions responsible for the high affinity of the β-anomer at atomic level. Further, the molecules showed good stability in murine and human blood plasma and hepatic metabolism, providing a basis for future development into antibacterial drugs.

Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic p53 Mutant Y220C.

The tumor suppressor protein p53 is inactivated in the majority of human cancers and remains a prime target for developing new drugs to reactivate its tumor suppressing activity for anticancer therapies. The oncogenic p53 mutant Y220C accounts for approximately 125,000 new cancer cases per annum and is one of the most prevalent p53 mutants overall. It harbors a narrow, mutationally induced pocket at the surface of the DNA-binding domain that destabilizes p53, leading to its rapid denaturation and aggregation. Here, we present the structure-guided development of high-affinity small molecules stabilizing p53-Y220C in vitro, along with the synthetic routes developed in the process, in vitro structure-activity relationship data, and confirmation of their binding mode by protein X-ray crystallography. We disclose two new chemical probes displaying sub-micromolar binding affinity in vitro, marking an important milestone since the discovery of the first small-molecule ligand of Y220C in 2008. New chemical probe JC744 displayed a K d = 320 nM, along with potent in vitro protein stabilization. This study, therefore, represents a significant advance toward high-affinity Y220C ligands for clinical evaluation.

Quantitative Validation and Application of the Photo-Cross-Linking Selection for Double-Stranded DNA-Encoded Libraries.

The DNA-encoded compound library (DEL) technology has accelerated the target hits discovery in new drug development. While affinity-based DEL selection can distinguish high-affinity ligands, moderate-affinity ligands are also potential drug candidates with further modifications. Herein, we designed a photo-cross-linking selection method for DELs with double-stranded DNA (dsDELs) to screen moderate-affinity ligands. We constructed two photo-cross-linking libraries with linkers of different lengths that connect a diazirine group to the DNA encoded compound. The diazirine group can be activated by UV irradiation and thus bond with the target protein in a reachable distance. In the model selection, the feasibility of the photo-cross-linking screening system was verified by qPCR and NGS technology. Both high-affinity and moderate-affinity ligands were successfully selected from the libraries.

Synergetic collision and space separation in microfluidic chip for efficient affinity-discriminated molecular selection

Efficient molecular selection is a prerequisite for generating molecular tools used in diagnosis, pathology, vaccinology, and therapeutics. Selection efficiency is thermodynamically highly dependent on the dissociation equilibrium that can be reached in a single round. Extreme shifting of equilibrium towards dissociation favors the retention of high-affinity ligands over those with lower affinity, thus improving the selection efficiency. We propose to synergize dual effects by deterministic lateral-displacement microfluidics, including the collision-based force effect and the two-dimensional (2D) separation-based concentration effect, to greatly shift the equilibrium. Compared with previous approaches, this system can remove more low- or moderate-affinity ligands and maintain most high-affinity ligands, thereby improving affinity discrimination in selection. This strategy is demonstrated on phage display in both experiment and simulation, and two peptides against tumor markers ephrin type-A receptor 2 (EphA2) and CD71 were obtained with high affinity and specificity within a single round of selection, which offers a promising direction for discovery of robust binding ligands for a wide range of biomedical applications.

Probing Factor Xa Protein-Ligand Interactions: Accurate Free Energy Calculations and Experimental Validations of Two Series of High-Affinity Ligands.

The accurate prediction of protein-ligand binding affinity belongs to one of the central goals in computer-based drug design. Molecular dynamics (MD)-based free energy calculations have become increasingly popular in this respect due to their accuracy and solid theoretical basis. Here, we present a combined study which encompasses experimental and computational studies on two series of factor Xa ligands, which enclose a broad chemical space including large modifications of the central scaffold. Using this integrated approach, we identified several new ligands with different heterocyclic scaffolds different from the previously identified indole-2-carboxamides that show superior or similar affinity. Furthermore, the so far underexplored terminal alkyne moiety proved to be a suitable non-classical bioisosteric replacement for the higher halogen-π aryl interactions. With this challenging example, we demonstrated the ability of the MD-based non-equilibrium free energy calculation approach for guiding crucial modifications in the lead optimization process, such as scaffold replacement and single-site modifications at molecular interaction hot spots.

Koumine regulates macrophage M1/M2 polarization via TSPO, alleviating sepsis-associated liver injury in mice

BackgroundTranslocator protein (TSPO) is an 18-kDa transmembrane protein found primarily in the mitochondrial outer membrane, and it is implicated in inflammatory responses, such as cytokine release. Koumine (KM) is an indole alkaloid extracted from Gelsemium elegans Benth. It has been reported to be a high-affinity ligand of TSPO and to exert anti-inflammatory and immunomodulatory effects in our recent studies. However, the protective effect of KM on sepsis-associated liver injury (SALI) and its mechanisms are unknown. Purpose: To explore the role of TSPO in SALI and then further explore the protective effect and mechanism of KM on SALI. MethodsThe effect of KM on the survival rate of septic mice was confirmed in mouse models of caecal ligation and puncture (CLP)-induced and lipopolysaccharide (LPS)-induced sepsis. The protective effect of KM on CLP-induced SALI was comprehensively evaluated by observing the morphology of the mouse liver and measuring liver injury markers. The serum cytokine content was detected in mice by flow cytometry. Macrophage polarization in the liver was examined using western blotting. TSPO knockout mice were used to explore the role of TSPO in sepsis liver injury and verify the protective effect of KM on sepsis liver injury through TSPO. ResultsKM significantly improved the survival rate of both LPS- and CLP-induced sepsis in mice. KM has a significant liver protective effect on CLP-induced sepsis in mice. KM treatment ameliorated liver ischaemia, improved liver pathological injuries, and decreased the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH) and proinflammatory cytokines in serum. Western blotting results showed that KM inhibited M1 polarization of macrophages and promoted M2 polarization. In TSPO knockout mice, we found that TSPO knockout can improve the survival rate of septic mice, ameliorate liver ischaemia, improve liver pathological injuries, and decrease the levels of ALT, AST, and LDH. In addition, TSPO knockout inhibits the M1 polarization of macrophages in the liver of septic mice and promotes M2 polarization and the serum levels of proinflammatory cytokines. Interestingly, in TSPO knockout septic mice, these protective effects of KM were no longer effective. ConclusionsWe report for the first time that TSPO plays a critical role in sepsis-associated liver injury by regulating the polarization of liver macrophages and reducing the inflammatory response. KM, a TSPO ligand, is a potentially desirable candidate for the treatment of SALI that may regulate macrophage M1/M2 polarization through TSPO in the liver.

Reactions of cisplatin and oxaliplatin with penicillin G: implications for drug inactivation and biological activity

Determination of the toxicity of compounds toward cancer cells is a frequent procedure in drug discovery. For metal complexes, which are often reactive prodrugs, care has to be taken to consider reactions with components of the cell culture medium that might change the speciation of the metal complex before it is taken up by the cells. Here, we consider possible reactions between the clinical platinum drugs cisplatin and oxaliplatin with penicillin G, an antibiotic added routinely to cell culture media to prevent bacterial contamination. Platinum has a high affinity for ligands with sulfur donors. Penicillin G is an unstable thioether that degrades in a range of pathways. Nuclear magnetic resonance (NMR) and UV–Vis absorption spectroscopic studies show that reactions with cisplatin can occur within minutes to hours at 310 K, but more slowly with oxaliplatin. The identities of the Pt- adducts were investigated by mass spectrometry. The marked effect on cytotoxicity of co-incubation of cisplatin with penicillin G was demonstrated for the HeLa human cervical cancer cell line. These studies highlight the possibility that reactions with penicillin G might influence the cytotoxic activity of metal complexes determined in culture media.Graphical abstract

Isothermal titration calorimetry determination of thermodynamics of binding of cocaine and its metabolites to humanized h2E2 anti-cocaine mAb

We analyzed the thermodynamics of binding of cocaine and several cocaine metabolites to a humanized anti-cocaine mAb (h2E2), which is under development for the treatment of cocaine use disorders, using isothermal titration calorimetry. The calculated equilibrium dissociation (binding) constants were consistent with previous findings using other methods. All three ligands that display high affinity (nM) binding to the mAb (cocaine, cocaethylene, and benzoylecgonine) displayed similar enthalpically driven binding with substantial enthalpy-entropy compensation. The increased affinity of the cocaethylene metabolite compared to cocaine and benzoylecgonine is mostly attributable to a substantially less negative entropic binding component for cocaethylene, resulting in a more favorable binding energy, and thus, a higher affinity. The much lower affinity cocaine metabolites, norcocaine and ecgonine methyl ester, have much lower binding enthalpies than the high affinity ligands, and in contrast to the three high affinity ligands, have favorable (positive) entropic thermodynamic components of binding. Surprisingly, approximately 3.7 molecules of norcocaine are bound per mAb Fab site, as determined by isothermal titration calorimetry. This is in contrast to the three high affinity ligands, which bound with the expected stoichiometry of one drug molecule bound per one mAb Fab site. The results are discussed in relation to the previously published Fab:benzoylecgonine crystal structure for this h2E2 mAb, and compared to the isothermal titration calorimetry results published previously using an unrelated anti-cocaine mAb, mAb08.

A convenient synthesis of (3S,3aR,5R,7aS,8S)-Hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-ol, a high-affinity nonpeptidyl ligand for highly potent HIV-1 protease inhibitors

We describe a practical synthesis of optically active (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-ol. This stereochemically defined 6-5-5 tricyclic heterocycle is an important high-affinity P2 ligand for a variety of highly potent HIV-1 protease inhibitors that show clinical potential. The key steps involve an enantioselective ring opening of meso carbic anhydride mediated by the cinchona alkaloid. The resulting optically active acid was reduced to optically active bicyclo[2.2.1]hept-5-ene derivative which was converted to the ligand alcohol by ozonolysis, reduction, and dehydration of the resulting primary alcohol followed by ozonolytic cleavage and reduction. Optically active ligand alcohol was obtained in high enantiomeric purity (99 % ee).

The β8 integrin EGF domains support a constitutive extended conformation, and the cytoplasmic domain impairs outside-in signaling.

Integrins are transmembrane proteins that transmit bi-directional signals across the cell membrane through global structural rearrangement among three different conformational states: bent, extended- closed, and extended-open conformations. However, the β8 integrin is distinctive and may adopt only one conformation, that is, extended-closed conformation, with high affinity for ligands under physiological conditions, and may not transmit bi-directional signals like other integrin members. It is unclear how different β8 domains affect its unique conformation and signaling. We swapped different domains of integrin β3 with those of β8 and investigated how they affected integrin ligand binding, global conformation, and outside-in signaling. We found that the β8 epidermal growth factor (EGF) domains increased integrin ligand binding ability and contributed to its extended conformation. By comparison, the β8 transmembrane and cytoplasmic domains had little effect on ligand binding or global conformation. The β8 EGF and transmembrane domains did not affect integrin-mediated cell adhesion, cell spreading, focal adhesion formation, or colocalization of integrin with other proteins, but the cytoplasmic domain had a defective effect on outside-in signaling. Our results showed that different domains of β8 play various roles on its unique conformation, ligand binding, and signaling, which are considered atypical among integrin members.

Development of a Deep Learning Generative Neural Network for Computer-Aided Design of Potential SARS-Cov-2 Inhibitors

Two generative deep learning models have been developed for the computer-aided design of potential inhibitors of the SARS-CoV-2 main protease (MPro), an enzyme critically important for the virus replication and transcription, and, therefore, presenting a promising target for the design of effective antiviral drugs. To solve this problem, we formed a training library of small molecules containing structural elements capable of providing specific and effective interactions of potential ligands with the SARS-CoV-2 MPro catalytic site. The architecture of generative models was developed and implemented to generate new high-affinity ligands of this functionally important SARS-CoV-2 protein. The neural network was trained and tested on the compounds from the training library, and the results of training and operation in two different generation modes were evaluated. The use of generative models in conjunction with the molecular docking demonstrated their great potential for filling the unexplored regions of the chemical space with novel molecules with pre-defined properties, which is confirmed by the obtained results according to which out of 4805 compounds generated by the neural network only one compound was present in the original data set.