Ligand Binding Selectivity Research Articles

Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations.

We present receptor hopping and receptor swapping free energy estimation protocols based on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands to two arbitrary receptors. The receptor hopping protocol, where a ligand is alchemically transferred from one receptor to another in one simulation, directly yields the ligand's binding selectivity free energy (BSFE) for the two receptors, which is the difference between the two individual binding free energies. In the receptor swapping protocol, the first ligand of a pair is transferred from one receptor to another while the second ligand is simultaneously transferred in the opposite direction. The receptor swapping free energy yields the differences in binding selectivity free energies of a set of ligands, which, when combined using a generalized DiffNet algorithm, yield the binding selectivity free energies of the ligands. We test these algorithms on host-guest systems and show that they yield results that agree with experimental data and are consistent with differences in absolute and relative binding free energies obtained by conventional methods. Preliminary applications to the selectivity analysis of molecular fragments binding to the trypsin and thrombin serine protease confirm the potential of the receptor swapping technology in structure-based drug discovery. The novel methodologies presented in this work are a first step toward streamlined and computationally efficient protocols for ligand selectivity optimization between mutants and homologous proteins.

Unveiling the structural mechanisms of nonpeptide ligand recognition and activation in human chemokine receptor CCR8.

The human CC chemokine receptor 8 (CCR8) is an emerging therapeutic target for cancer immunotherapy and autoimmune diseases. Understanding the molecular recognition of CCR8, particularly with nonpeptide ligands, is valuable for drug development. Here, we report three cryo-electron microscopy structures of human CCR8 complexed with Gi trimers in the ligand-free state or activated by nonpeptide agonists LMD-009 and ZK 756326. A conserved Y1.39Y3.32E7.39 motif in the orthosteric binding pocket is shown to play a crucial role in the chemokine and nonpeptide ligand recognition. Structural and functional analyses indicate that the lack of conservation in Y1143.33 and Y1724.64 among the CC chemokine receptors could potentially contribute to the selectivity of the nonpeptide ligand binding to CCR8. These findings present the characterization of the molecular interaction between a nonpeptide agonist and a chemokine receptor, aiding the development of therapeutics targeting related diseases through a structure-based approach.

Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A2A receptor

Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A2A receptor (A2AR) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A2AR in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A2AR. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A2AR.

Molecular Dynamics Simulation Study of the Selective Inhibition of Coagulation Factor IXa over Factor Xa.

Thromboembolic disorders, arising from abnormal coagulation, pose a significant risk to human life in the modern world. The FDA has recently approved several anticoagulant drugs targeting factor Xa (FXa) to manage these disorders. However, these drugs have potential side effects, leading to bleeding complications in patients. To mitigate these risks, coagulation factor IXa (FIXa) has emerged as a promising target due to its selective regulation of the intrinsic pathway. Due to the high structural and functional similarities of these coagulation factors and their inhibitor binding modes, designing a selective inhibitor specifically targeting FIXa remains a challenging task. The dynamic behavior of protein-ligand interactions and their impact on selectivity were analyzed using molecular dynamics simulation, considering the availability of potent and selective compounds for both coagulation factors and the co-crystal structures of protein-ligand complexes. Throughout the simulations, we examined ligand movements in the binding site, as well as the contact frequencies and interaction fingerprints, to gain insights into selectivity. Interaction fingerprint (IFP) analysis clearly highlights the crucial role of strong H-bond formation between the ligand and D189 and A190 in the S1 subsite for FIXa selectivity, consistent with our previous study. This dynamic analysis also reveals additional FIXa-specific interactions. Additionally, the absence of polar interactions contributes to the selectivity for FXa, as observed from the dynamic profile of interactions. A contact frequency analysis of the protein-ligand complexes provides further confirmation of the selectivity criteria for FIXa and FXa, as well as criteria for binding and activity. Moreover, a ligand movement analysis reveals key interaction dynamics that highlight the tighter binding of selective ligands to the proteins compared to non-selective and inactive ligands.

Metal-Ligand Interactions and Their Roles in Controlling Nanoparticle Formation and Functions.

ConspectusFunctional nanoparticles (NPs) have been studied extensively in the past decades for their unique nanoscale properties and their promising applications in advanced nanosciences and nanotechnologies. One critical component of studying these NPs is to prepare monodisperse NPs so that their physical and chemical properties can be tuned and optimized. Solution phase reactions have provided the most reliable processes for fabricating such monodisperse NPs in which metal-ligand interactions play essential roles in the synthetic controls. These interactions are also key to stabilizing the preformed NPs for them to show the desired electronic, magnetic, photonic, and catalytic properties. In this Account, we summarize some representative organic bipolar ligands that have recently been explored to control NP formation and NP functions. These include aliphatic acids, alkylphosphonic acids, alkylamines, alkylphosphines, and alkylthiols. This ligand group covers metal-ligand interactions via covalent, coordination, and electrostatic bonds that are most commonly employed to control NP sizes, compositions, shapes, and properties. The metal-ligand bonding effects on NP nucleation rate and growth can now be more thoroughly investigated by in situ spectroscopic and theoretical studies. In general, to obtain the desired NP size and monodispersity requires rational control of the metal/ligand ratios, concentrations, and reaction temperatures in the synthetic solutions. In addition, for multicomponent NPs, the binding strength of ligands to various metal surfaces needs to be considered in order to prepare these NPs with predesigned compositions. The selective ligand binding onto certain facets of NPs is also key to anisotropic growth of NPs, as demonstrated in the synthesis of one-dimensional nanorods and nanowires. The effects of metal-ligand interactions on NP functions are discussed in two aspects, electrochemical catalysis for CO2 reduction and electronic transport across NP assemblies. We first highlight recent advances in using surface ligands to promote the electrochemical reduction of CO2. Several mechanisms are discussed, including the modification of the catalyst surface environment, electron transfer through the metal-organic interface, and stabilization of the CO2 reduction intermediates, all of which facilitate selective CO2 reduction. These strategies lead to better understanding of molecular level control of catalysis for further catalyst optimization. Metal-ligand interaction in magnetic NPs can also be used to control tunneling magnetoresistance properties across NPs in NP assemblies by tuning NP interparticle spacing and surface spin polarization. In all, metal-ligand interactions have yielded particularly promising directions for tuning CO2 reduction selectivity and for optimizing nanoelectronics, and the concepts can certainly be extended to rationalize NP engineering at atomic/molecular precision for the fabrication of sensitive functional devices that will be critical for many nanotechnological applications.

Selective polypeptide ligand binding to the extracellular surface of the transmembrane domains of the class B GPCRs GLP-1R and GCGR

Crystal and cryo-EM structures of the glucagon-like peptide-1 receptor (GLP-1R) and glucagon receptor (GCGR) bound with their peptide ligands have been obtained with full-length constructs, indicating that the extracellular domain (ECD) is indispensable for specific ligand binding. This article complements these data with studies of ligand recognition of the two receptors in solution. Paramagnetic NMR relaxation enhancement measurements using dual labeling with fluorine-19 probes on the receptor and nitroxide spin labels on the peptide ligands provided new insights. The glucagon-like peptide-1 (GLP-1) was found to interact with GLP-1R by selective binding to the extracellular surface. The ligand selectivity toward the extracellular surface of the receptor was preserved in the transmembrane domain (TMD) devoid of the ECD. The dual labeling approach further provided evidence of cross-reactivity of GLP-1R and GCGR with glucagon and GLP-1, respectively, which is of interest in the context of medical treatments usingcombinations of the two polypeptides.

Ligand-induced activation and G protein coupling of prostaglandin F2α receptor

Prostaglandin F2α (PGF2α), an endogenous arachidonic acid metabolite, regulates diverse physiological functions in many tissues and cell types through binding and activation of a G-protein-coupled receptor (GPCR), the PGF2α receptor (FP), which also is the primary therapeutic target for glaucoma and several other diseases. Here, we report cryo-electron microscopy (cryo-EM) structures of the human FP bound to endogenous ligand PGF2α and anti-glaucoma drugs LTPA and TFPA at global resolutions of 2.67 Å, 2.78 Å, and 3.14 Å. These structures reveal distinct features of FP within the lipid receptor family in terms of ligand binding selectivity, its receptor activation, and G protein coupling mechanisms, including activation in the absence of canonical PIF and ERY motifs and Gq coupling through direct interactions with receptor transmembrane helix 1 and intracellular loop 1. Together with mutagenesis and functional studies, our structures reveal mechanisms of ligand recognition, receptor activation, and G protein coupling by FP, which could facilitate rational design of FP-targeting drugs.

Abstract 2756: Custom G4 DNA microarray can determine large-scale binding selectivity of small molecules and proteins to oncogene G-quadruplexes

Abstract G-quadruplexes are novel DNA secondary structures that are formed in guanine-rich genomic regions with functional importance in cancers, such as human telomeres and oncogene promoters. G-quadruplexes adopt globular structures distinct from duplex B-DNA and their structural diversity suggests specific recognition. G-quadruplexes have become attractive drug targets because they provide a means of addressing otherwise undruggable targets. As one example, MYC is an important oncogene that is difficult to target by traditional drug design; however, its regulation involves a promoter G-quadruplex (MycG4) that is a potential drug target. 3,6-bis(1-Methyl-4-vinylpyridinium) carbazole diiodide (BMVC) is the first fluorescent probe developed for detecting G-quadruplex structures in cells and has been tested for cancer cell diagnosis. Although it was designed to detect the G-quadruplexes formed in human telomeres, we found BMVC binds to the MYC promoter G-quadruplex (MycG4) with higher affinity and specificity. We determined the high-resolution NMR K+ solution structure of the 2:1 BMVC-MycG4 complex showing a novel conformational adjustment of BMVC for an optimal binding to G-quadruplexes. Intriguingly, BMVC binds the 5’-end of MycG4 with higher affinity, but it binds the 3’-end with greater sequence selectivity. To determine ligand-binding selectivity on a large-scale, we designed a new custom G-quadruplex microarray platform with more than 25,000 potential oncogene G4 sequences and mutants. The new microarray was able to systematically assess binding affinity and selectivity of drugs targeted to G4s like the G-quadruplex involved in MYC regulation. The microarray results show that BMVC preferentially binds to the parallel type of G-quadruplexes, especially MycG4. Importantly, a strong sequence selectivity of BMVC for a 3’ flanking T was observed, consistent with the NMR data. The new microarray was also able to systematically assess binding of proteins and antibodies in a high-throughput and unbiased manner, and we tested the G-quadruplex binding proteins FANCJ, PIF1, BLM, DHX36, WRN, IGF2, CNBP, nucleolin, as well as the G-quadruplex-specific antibody BG4. In conclusion, we establish the custom G4 DNA microarray which can be used to determine binding selectivity of small molecules and proteins to oncogene G-quadruplexes in large-scale and high-throughput. Citation Format: Guanhui Wu, Luying Chen, Kristen Huseman, Desiree Tillo, Sreejana Ray, Ta-Chau Chang, John S. Schneekloth, Charles Vinson, Danzhou Yang. Custom G4 DNA microarray can determine large-scale binding selectivity of small molecules and proteins to oncogene G-quadruplexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2756.

Quantum Mechanical Assessment of Protein-Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory.

Hydrogen bonds (HB)s are the most abundant motifs in biological systems. They play a key role in determining protein-ligand binding affinity and selectivity. We designed two pharmaceutically beneficial HB databases, database A including ca. 12,000 protein-ligand complexes with ca. 22,000 HBs and their geometries, and database B including ca. 400 protein-ligand complexes with ca. 2200 HBs, their geometries, and bond strengths determined via our local vibrational mode analysis. We identified seven major HB patterns, which can be utilized as a de novo QSAR model to predict the binding affinity for a specific protein-ligand complex. Glycine was reported as the most abundant amino acid residue in both donor and acceptor profiles, and N-H⋯O was the most frequent HB type found in database A. HBs were preferred to be in the linear range, and linear HBs were identified as the strongest. HBs with HB angles in the range of 100-110°, typically forming intramolecular five-membered ring structures, showed good hydrophobic properties and membrane permeability. Utilizing database B, we found a generalized Badger's relationship for more than 2200 protein-ligand HBs. In addition, the strength and occurrence maps between each amino acid residue and ligand functional groups open an attractive possibility for a novel drug-design approach and for determining drug selectivity and affinity, and they can also serve as an important tool for the hit-to-lead process.

Binding and selectivity studies of phosphatidylinositol 3-kinase (PI3K) inhibitors

Overexpression of the Phosphatidylinositol 3-kinase (PI3K) proteins have been observed in cancer cells. Targeting the phosphatidylinositol 3-kinase (PI3K) signaling transduction pathway by inhibition of the PI3K substrate recognition sites has been proved to be an effective approach to block cancer progression. Many PI3K inhibitors have been developed. Seven drugs have been approved by the US FDA with a mechanism of targeting the phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway. In this study, we used docking tools to investigate selective binding of ligands toward four different subtypes of PI3Ks (PI3Kα, PI3Kβ, PI3Kγ and PI3Kδ). The affinity predicted from both the Glide dock and the Movable-Type (MT)-based free energy calculations agreed well with the experimental data. The validation of our predicted methods with a large dataset of 147 ligands showed very small mean errors. We identified residues that may dictate the subtype-specific binding. Particularly, residues Asp964, Ser806, Lys890 and Thr886 of PI3Kγ might be utilized for PI3Kγ-selective inhibitor design. Residues Val828, Trp760, Glu826 and Tyr813 may be important for PI3Kδ-selective inhibitor binding.

Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding.

Novel agents to treat invasive fungal infections are urgently needed because the small number of established targets in pathogenic fungi makes the existing drug repertoire particularly vulnerable to the emergence of resistant strains. Recently, we reported that Candida albicans Bdf1, a bromodomain and extra-terminal domain (BET) bromodomain with paired acetyl-lysine (AcK) binding sites (BD1 and BD2) is essential for fungal cell growth and that an imidazopyridine (1) binds to BD2 with selectivity versus both BD1 and human BET bromodomains. Bromodomain binding pockets contain a conserved array of structural waters. Molecular dynamics simulations now reveal that one water molecule is less tightly bound to BD2 than to BD1, explaining the site selectivity of 1. This insight is useful in the performance of ligand docking studies to guide design of more effective Bdf1 inhibitors, as illustrated by the design of 10 new imidazopyridine BD2 ligands 1a-j, for which experimental binding and site selectivity data are presented.

Analysis of Binding Determinants for Different Classes of Competitive and Noncompetitive Inhibitors of Glycine Transporters.

Glycine transporters are interesting therapeutic targets as they play significant roles in glycinergic and glutamatergic systems. The search for new selective inhibitors of particular types of glycine transporters (GlyT-1 and GlyT-2) with beneficial kinetics is hampered by limited knowledge about the spatial structure of these proteins. In this study, a pool of homology models of GlyT-1 and GlyT-2 in different conformational states was constructed using the crystal structures of related transporters from the SLC6 family and the recently revealed structure of GlyT-1 in the inward-open state, in order to investigate their binding sites. The binding mode of the known GlyT-1 and GlyT-2 inhibitors was determined using molecular docking studies, molecular dynamics simulations, and MM-GBSA free energy calculations. The results of this study indicate that two amino acids, Gly373 and Leu476 in GlyT-1 and the corresponding Ser479 and Thr582 in GlyT-2, are mainly responsible for the selective binding of ligands within the S1 site. Apart from these, one pocket of the S2 site, which lies between TM3 and TM10, may also be important. Moreover, selective binding of noncompetitive GlyT-1 inhibitors in the intracellular release pathway is affected by hydrophobic interactions with Ile399, Met382, and Leu158. These results can be useful in the rational design of new glycine transporter inhibitors with desired selectivity and properties in the future.

Affinity variation in the interactions of tryptophan- β-cyclodextrin-platinum complex with G-quadruplex and duplex DNAs

DNA forms non-canonical Guanine-rich-quadruplex structures that play crucial roles such as maintenance of the telomere, transcription, and replication. Selective binding of small molecular ligands to G-quadruplexes and stabilization of them gain importance in the control of cell proliferation and development of therapeutics. In this paper, we report the synthesis of a tryptophan-β-cyclodextrin complex and its platinum complex. The binding interaction of the synthesized Trp-β-CD-Pt compound with various DNAs, including a duplex DNA and three quadruplexes, are investigated. The binding of the compound to quadruplexes shows a general increase in the binding strength compared to the strength of binding with the duplex, CT-DNA. The compound reveals the strongest binding with kit22. An enhancement of fluorescence is generally observed when the ligand binds to all the DNAs, except myc22. The structure of the host: guest complex with Berberine, a model G-quadruplex binding ligand, is investigated using 2 D ROESY spectroscopy. The host: guest binding is strong and the DNA interaction does not extract much of the Berberine molecule from the complex. The differential bindings of the ligand in free- and Berberine-loaded forms with different G-quadruplexes are discussed in detail based on binding strengths and the modulation of fluorescence. Communicated by Ramaswamy H. Sarma

Chimeric Ligands of Pili and Lectin A Inhibit Tolerance, Persistence, and Virulence Factors of Pseudomonas aeruginosa over a Wide Range of Phenotypes.

Bacteria readily form resilient phenotypes to counter environmental and antibiotic stresses. Here, we demonstrate a class of small molecules that inhibit a wide range of Pseudomonas aeruginosa phenotypes and enable antibiotics to kill previously tolerant bacteria, preventing the transition of tolerant bacteria into a persistent population. We identified two proteins, type IV pili and lectin LecA, as receptors for our molecules by methods including a new label-free assay based on bacterial motility sensing the chemicals in the environment, the chemical inhibition of bacteriophage adsorption on pili appendages of bacteria, and fluorescence polarization. Structure–activity relationship studies reveal a molecule that inhibits only pili appendage and a class of chimeric ligands that inhibit both LecA and pili. Important structural elements of the ligand are identified for each protein. This selective ligand binding identifies the phenotypes each protein receptor controls. Inhibiting LecA results in reducing biofilm formation, eliminating small colony variants, and is correlated with killing previously tolerant bacteria. Inhibiting pili appendages impedes swarming and twitching motilities and pyocyanin and elastase production. Because these phenotypes are controlled by a broad range of signaling pathways, this approach simultaneously controls the multiple signaling mechanisms preventing bacteria to elude antibiotic treatments.

Possible catalytic activity of N,N-coordinated mono-cationic copper bound Pyrazol-1-yl(1H-pyrrol-2-yl)methanone complex: a computational study

Organic ligand-based transition metal coordinated complexes have been of paramount importance. They have found a lot of utilities in catalysis, bond activation, dye-sensitized solar cells, etc. Focusing on the so-called noble metal or coinage metal and keeping in mind the inexpensive single metal atom based catalyst, copper bound complexes are considered for adsorption of gas molecules and bond activation therein. Here, we have studied the interaction between a [Cu–NN] complex (N,N-coordinated mono-cationic copper bound Pyrazol-1-yl(1H-pyrrol-2-yl)methanone) and different gas molecules as ligands, such as L = H2, N2, CO, H2O, C2H4 and C2H2, which are industrially and environmentally important. Our computational investigation infers that these ligands are effective in electronic interactions and optical properties of the complex. The stability, geometry and the bonding nature in L bound [Cu–NN] complexes are studied to check their viability at room temperature. The [Cu–NN] complex can bind small gas molecules as ligands, viz., H2, N2, CO, H2O, C2H4 and C2H2, in a thermodynamically favorable way and the complexation induces bond activation within the ligands in the bound state as compared to their free state. All the [L–Cu–NN] complexes along with the bare complex show broadband optical absorption in the ultraviolet–visible (UV–Vis) domains. Furthermore, selective ligand binding has modulated the Fermi energy level resulting in an enhanced chemical reactivity of the [Cu–NN] complex.

Diversity in the Interaction of Amino Acid- and Peptide-Based Hydroxamic Acids with Some Platinum Group Metals in Solution.

Complexes that incorporate both ligand(s) and metal(s) exhibiting cytotoxic activity can especially be interesting to develop multifunctional drug molecules with desired activities. In this review, the limited number of solution results collected in our laboratory on the complexes of Pd(II) and two other platinum group metals—the half-sandwich type, [(η6-p-cym)Ru(H2O)3]2+, and [(η5-Cp*)Rh(H2O)3]2+—with hydroxamic acid derivatives of three amino acids, two imidazole analogues, and four small peptides are summarized and evaluated. Unlike the limited number of coordination sites of these metal ions (four and three for Pd(II) and the organometallic cations, respectively), the ligands discussed here offer a relatively high number of donor atoms as well as variation in their position within the ligands, resulting in a large versatility of the likely coordination modes. The review, besides presenting the solution equilibrium results, also discusses the main factors, such as (N,N) versus (O,O) chelate; size of chelate; amino-N versus imidazole-N; primary versus secondary hydroxamic function; differences between hydrolytic ability of the metal ions studied; and hydrolysis of the coordinated peptide hydroxamic acids in their Pd(II) complexes, which all determine the coordination modes present in the complexes formed in measurable concentrations in these systems. The options for the quantitative evaluation of metal binding effectivity and selectivity of the various ligands and the comparison with each other by using solution equilibrium data are also discussed.

Luminescence and Stability Enhancement of Inorganic Perovskite Nanocrystals via Selective Surface Ligand Binding.

Colloidal lead halide perovskite nanocrystals (NCs) have recently emerged as one of the most promising light-emitting materials for optoelectronic devices with outstanding performance. However, the facile detachment of surface capping organic ligands from these NCs leads to very poor colloidal stability and durability. This is mainly due to the weak interfacial interactions between the inorganic perovskite core and ligands, high density of surface defect states, and aggregation of NCs. Here, using a combination of time-resolved laser spectroscopy and density functional theory (DFT) calculations, we explored the major impact of surface orientations and terminations for both CsPbBr3 and Cs4PbBr6 NCs not only on the interfacial binding affinities with organic ligands but also on surface defect formation and NC aggregation. By rationalizing that surface trap states are responsible for the decrease in photoluminescence (PL) upon fabrication and purification, we propose a powerful ligand-engineering strategy for eliminating these trap states and preventing the aggregation of CsPbBr3 and Cs4PbBr6 NCs. Interestingly, we find that the surface orientation and dimensionality determine the degree of interfacial interactions between the inorganic perovskite core and ligands and subsequently control the overall PL intensity and NC stability. Our results demonstrate that a treatment of as-synthesized CsPbBr3 NCs consisting of the addition of extra oleylammonium bromide (OAmBr) as a capping ligand, allows the CsPbBr3 NCs to retain their green emission with increased PL intensity and quantum yields and improves colloidal durability. On the other hand, the ultraviolet emissions of Cs4PbBr6 NCs are effectively increased upon addition of extra cesium oleate (CsOL) as the trap states induced by surface cesium ions are largely reduced by the formation of Cs-O bonds. Our work provides a robust and adequate ligand engineering approach to significantly enhance the optical behavior of perovskite NCs with different dimensionalities and various compositions and to achieve more efficient and stable light-harvesting devices.

Theoretical investigation of selective ligand binding mode of galanin receptors

The Galaninergic system consist of Galanin and its receptors, involved in neuromodulation and neurotransmission. Galanin regulate its physiologic and pathologic functions by interacting with three G-protein coupled receptors; GalR1, GalR2 and GalR3. The widespread distribution of Galanin and its receptor subtypes in central and peripheral nervous system makes them an attractive drug target for the treatment of neurological diseases. However, subtypes selective ligands paucity and little structural information related to either Galanin receptors and Galanin receptor-ligand complexes hampered the structure-based drug design. Thus computational modeling characterization strategy was utilized for Galanin receptor 3D structure prediction and subtypes ligands binding selectivity. Reported ligands with experimental activity were docked against the homology model of Galanin receptors. Further, the MD simulation and binding free energy calculation were carried out to determine the binding interactions pattern consistency and selectivity towards receptor subtype. Results of binding free energy of per residue indicate key contribution of GalR1 Phe115 and His267 in the selective binding of ligands while Tyr103, Tyr270 and His277 play major role in the selective binding of GalR3 ligands. Our study provide rationale for further in silico virtual screening of small molecules for the development of selective ligands against Galanin receptor subtypes. Communicated by Ramaswamy H. Sarma

Abstract 291: Development of optimized chemical probes targeting PI3Ka to deconvolute the role of class I PI3Ks isoforms in insulin signaling

Abstract Phosphatidylinositol-3-kinase (PI3K) activity is aberrant in tumors, and PI3K inhibitors are investigated as cancer therapeutics.[1-5] The major obstacles to the successful implementation of PI3K-targeted cancer therapy are on-target adverse effects on insulin signaling. Isotype selective PI3K inhibitors have been exploited to answer fundamental questions regarding the role of PI3K isoforms in cell biology. However, the availability of claimed isoform-selective PI3Kα inhibitors is limited to BYL719 (Alpelisib)[6] and GDC0032 (Taselisib)[7], which do not maintain PI3Kα selectivity at a concentration required in cellular experimental settings and clinical applications. Highly selective PI3Kα inhibitors are expected to represent ideal tools to elucidate the role of PI3Kα isoform in tumor development and insulin signaling. As the systemic inactivation of PI3Kα is embryonic lethal, genetic approaches are currently limited to organ-specific targeting, and a specific inactivation of PI3Kα in an adult organism has not been achieved up-to-date. Herein, we generate high-quality PI3Kα chemical probes to dissect the role of PI3Kα in cancer and metabolism. We exploit covalent inhibitors, permanently blocking target functions, as a strategy to enhance the ligand binding selectivity for proteins in the same family. The non-conserved nucleophilic amino acid Cys862 in PI3Kα represents a promising target for covalent modifiers. We converted the reversible scaffold of PQR514[5] into irreversible compounds. An extensive Structure Activity Relationship (SAR) study was performed using CNX-1351[8] reacting group and introducing different heteroaliphatic rings in the linker. X-ray crystallography and bottom-up LC-MS/MS based proteomics validated the covalent modification of Cys862. Our pilot chemical probes exceeded in vitro and cellular potency over CNX-1351. The generation of a novel class of covalent PI3Kα-specific inhibitors with improved selectivity and persistency of PI3Kα-inhibition will shed light on the role of PI3Kα in cancer and metabolism. Our results will pave the way for the dissociation of PI3Ki antitumor activity from adverse effects on insulin action. [1] Beaufils F et al. J Med Chem. 2017, 60 (17), 7524-7538. [2] Rageot R et al. J Med Chem. 2019, 62 (13), 6241-6261. [3] Wymann MP et al. Nat Rev Mol Cell Biol. 2008, 9 (2), 62-176. [4] Marone R et al. Biochim Biophys Acta. 2008, 1784 (1), 159-185. [5] Borsari C et al. ACS Med Chem Lett. 2019, 10 (10), 1473-1479. [6] Markham A Drugs 2019, 79 (11), 1249-1253. [7] Zumsteg ZS et al. Clin Cancer Res. 2019, 22 (8), 2009-2019. [8] Nacht M et al. J Med Chem. 2013, 56 (3), 712-721. Citation Format: Martina De Pascale, Chiara Borsari, Erhan Keles, Jacob McPhail, Alexander Schäfer, Rohitha Sriramaratnam, Matthias Gstaiger, John Burke, Matthias Wymann. Development of optimized chemical probes targeting PI3Ka to deconvolute the role of class I PI3Ks isoforms in insulin signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 291.

Factors Governing Selectivity of Dopamine Receptor Binding Compounds for D2R and D3R Subtypes

Targeting the D3 dopamine receptor (D3R) is a promising pharmacotherapeutic strategy for the treatment of many disorders. The structure of the D3R is similar to the D2 dopamine receptor (D2R), especially in the transmembrane spanning regions that form the orthosteric binding site, making it difficult to identify D3R selective pharmacotherapeutic agents. Here, we examine the molecular basis for the high affinity D3R binding and D3R vs D2R binding selectivity of substituted phenylpiperazine thiopheneamides. We show that removing the thiophenearylamide portion of the ligand consistently decreases the affinity of these ligands at D3R, while not affecting their affinity at the D2R. Our long (>10 μs) molecular dynamics simulations demonstrated that both dopamine receptor subtypes adopt two major conformations that we refer to as closed or open conformations, with D3R sampling the open conformation more frequently than D2R. The binding of ligands with conjoined orthosteric-allosteric binding moieties causes the closed conformation to populate more often in the trajectories. Also, significant differences were observed in the extracellular loops (ECL) of these two receptor subtypes leading to the identification of several residues that contribute differently to the ligand binding for the two receptors that could potentially contribute to ligand binding selectivity. Our observations also suggest that the displacement of ordered water in the binding pocket of D3R contributes to the affinity of the compounds containing an allosteric binding motif. These studies provide a better understanding of how a bitopic mode of engagement can determine ligands that bind selectively to D2 and D3 dopamine receptor subtypes.