scholarly journals Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via New In Silico Methodologies

2020 ◽  
Author(s):  
Michael L. Drummond ◽  
Andrew Henry ◽  
Huifang Li ◽  
Christopher I. Williams
Keyword(s):  
Protein Degradation ◽  
Case Studies ◽  
Ternary Complex ◽  
Ternary Complexes ◽  
Complex Structures ◽  
Retrospective Case ◽  
Ternary Complex Formation ◽  
Protein Pockets ◽  
The Many ◽  
Improved Accuracy

ABSTRACTExtending upon our previous publication (Drummond and Williams, J. Chem. Inf. Model. 2019, 59, 1634), in this work two additional computational methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates a clustering procedure uniquely suited for considering ternary complexes. Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. Techniques to further improve this performance for particularly troublesome cases are suggested and validated. This demonstrated ability to reliably reproduce known crystallographic ternary complex structures is further established through modeling of a newly released crystal structure. Moreover, for the far more common scenario where the structure of the ternary complex intermediate is unknown, the methods detailed in this work nonetheless consistently yield results that reliably follow experimental protein degradation trends, as established through seven retrospective case studies. These various case studies cover challenging yet common modeling situations, such as when the precise orientation of the PROTAC binding moiety in one (or both) of the protein pockets has not been experimentally established. Successful results are presented for one PROTAC targeting many proteins, for different possible PROTACs targeting the same protein, and even for degradation effected by an E3 ligase that has not been structurally characterized in a ternary complex. Overall, the computational modeling approaches detailed in this work should greatly facilitate PROTAC screening and design efforts, so that the many advantages of a PROTAC-based degradation approach can be effectively utilized both rapidly and at reduced cost.

scholarly journals Binding characteristics of pro-insulin-like growth factor-II from cancer patients: binary and ternary complex formation with IGF binding proteins-1 to -6

2000 ◽  
Vol 165 (2) ◽  
pp. 253-260 ◽  
Author(s):  
JJ Bond ◽  
S Meka ◽  
RC Baxter
Keyword(s):  
Complex Formation ◽  
Ternary Complex ◽  
Binding Proteins ◽  
Ternary Complexes ◽  
Binary Complex ◽  
Igf Binding Proteins ◽  
Ternary Complex Formation ◽  
Binary Complexes ◽  
Igf Binding ◽  
Igfbp 3

Many tumours secrete IGF-II in incompletely processed precursor forms. The ability of these pro-IGF-II forms to complex with the six IGF binding proteins (IGFBPs) is poorly understood. In this study, pro-IGF-II has been extracted from the serum and tumour tissue of two patients with non-islet cell tumour hypoglycaemia. These samples were used to study binary complex formation with IGFBPs-1 to -6 using competitive IGF-II binding assays and ternary complex formation with IGFBP-3 and IGFBP-5. In each case, IGFBPs-1 to -6 showed little difference in their ability to form binary complexes with recombinant IGF-II or tumour-derived pro-IGF-II forms, when the preparations were standardised according to IGF-II immunoreactivity. As previously described, ternary complex formation by acid-labile subunit (ALS) with IGFBP-3 and pro-IGF-II was greatly decreased compared with complex formation with mature IGF-II. In contrast, ALS bound similarly to IGFBP-5 in the presence of pro-IGF-II and mature IGF-II. These studies suggest that pro-IGF-II preferentially forms binary complexes with IGFBPs, and ternary complexes with IGFBP-5, rather than ternary complexes with IGFBP-3 as seen predominantly in normal serum. This may increase the tissue availability of serum pro-IGF-II, allowing its insulin-like potential to be realised.

scholarly journals Characterization of the binding defect in insulin-like growth factor binding protein-3 from pregnancy serum

1993 ◽  
Vol 294 (3) ◽  
pp. 847-852 ◽  
Author(s):  
R C Baxter ◽  
A M Suikkari ◽  
J L Martin
Keyword(s):  
Growth Factor ◽  
Complex Formation ◽  
Ternary Complex ◽  
Binding Protein ◽  
Ternary Complexes ◽  
Insulin Like Growth Factor ◽  
Ternary Complex Formation ◽  
Igf I ◽  
Igf Binding ◽  
Igfbp 3

During pregnancy, insulin-like growth factor (IGF) binding protein-3 (IGFBP-3) undergoes proteolysis, rendering it undetectable by radioligand binding techniques. This study examines the physical and functional defect in pregnancy IGFBP-3. Ternary complex formation has been measured by the binding of the acid-labile subunit of the circulating IGFBP-3 complex, which also requires IGF-I or IGF-II binding. IGF-depleted pregnancy IGFBP-3, prepared by size-exclusion chromatography at low pH, could not form a ternary complex in the presence of [Tyr60]IGF-I or of an IGF-I analogue extensively altered in the A-domain, whereas analogues altered in the C- or D-domains complexed as well as native IGF-I. After purification by immunoaffinity chromatography, non-pregnancy and pregnancy IGFBP-3 formed ternary complexes with IGF-I equally well, although the pregnancy-proteolysed protein appeared degraded to approximately 30 kDa. On analysis by affinity labelling, cross-linked ternary complexes containing non-pregnancy or pregnancy IGFBP-3 were predominantly 135-140 kDa, with an additional complex of 110-115 kDa in the pregnancy preparation. After reverse-phase h.p.l.c., affinity-isolated pregnancy IGFBP-3 was inactive, whereas the protein from non-pregnancy serum retained activity. Thus pregnancy-proteolysed IGFBP-3 is altered in its specificity for IGF analogues, and is more labile than non-pregnancy IGFBP-3, but shows little impairment in normal IGF binding or ternary complex formation.

scholarly journals Development of an N-Terminal BRD4 Bromodomain-Targeted Degrader

2021 ◽  
Author(s):  
Anand Divakaran ◽  
Huda Zahid ◽  
Wenwei Lin ◽  
Taosheng Chen ◽  
Dan Harki ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Small Molecules ◽  
Ubiquitin Ligase ◽  
Ternary Complex ◽  
Selective Inhibitor ◽  
Selective Degradation ◽  
Ternary Complex Formation ◽  
Native Proteins ◽  
Bet Inhibitors ◽  
Ubiquitin Ligase E3

Targeted protein degradation is a powerful induced-proximity tool to control cellular concentrations of native proteins using small molecules. However, the design of selectivity in protein degradation remains challenging. In the case of Bromodomain and Extra-Terminal (BET) family proteins, BRD4 has emerged as the primary therapeutic target over other family members BRD2, 3 and T, but strategies to selectively degrade BRD4 rely on the use of pan-BET inhibitors optimized for BRD4:E3 protein-ubiquitin ligase (E3) ternary complex formation. Here, we report a potent and selective inhibitor for the first bromodomain of BRD4, iBRD4-BD1 (IC50 = 12 nM, 23-6200-fold intra-BET selectivity). We further use this novel inhibitor to develop dBRD4-BD1 that induces selective degradation of BRD4 at a DC50 of 280 nM. The design of BRD4 selectivity up-front enables the study of BRD4 biology in the absence of wider BET-inhibition, simplifies design of future BRD4-selective degraders as new E3 recruiting ligands are discovered, and provides a tool to design additional heterobifunctional BRD4-selective probes.

scholarly journals Potentiometric Studies of Mixed Copper(II) Complexes with δ-Aminolevulinic Acid and Some Selected Peptides

2020 ◽  
Vol 32 (5) ◽  
pp. 1251-1254
Author(s):  
Salhah D. Al-Qahtani
Keyword(s):  
Concentration Distribution ◽  
Ternary Complex ◽  
Aminolevulinic Acid ◽  
Ternary Complexes ◽  
Mixed Ligand ◽  
Potentiometric Studies ◽  
Binary And Ternary Complexes ◽  
Ternary Complex Formation ◽  
Relative Stabilization ◽  
The Stability

Ternary complex formation in the system Cu(II)-ALA-L (ALA = δ-aminolevulinic acid drug; L = peptides) has been studied by pH-potentiometrically at 25 ± 0.1 ºC with I = 0.10 mol L-1 NaCl. The stability constants of binary and ternary complexes were calculated and interpretated. The concentration distribution of the complexes in solution was graphically presented using the HySS program. In addition, the values of Δlog K, log X and relative stabilization percentage (% R.S.) for the mixed-ligand complexes studied have been evaluated and discussed.

Binding Mechanism and Structural Insights into the Identified Protein Target of Covid-19 with In-Vitro Effective Drug Ivermectin

2020 ◽  
Author(s):  
Parth Sarthi Sen Gupta ◽  
Satyaranjan Biswal ◽  
Saroj Kumar Panda ◽  
Abhik Kumar Ray ◽  
Malay Kumar Rana
Keyword(s):  
Ternary Complex ◽  
Bound State ◽  
Molecular Target ◽  
Cooperative Interaction ◽  
Effective Drug ◽  
Rna Dependent Rna Polymerase ◽  
Protein Target ◽  
Ternary Complex Formation ◽  
Structural Insights

<p>While an FDA approved drug Ivermectin was reported to dramatically reduce the cell line of SARS-CoV-2 by ~5000 folds within 48 hours, the precise mechanism of action and the COVID-19 molecular target involved in interaction with this in-vitro effective drug are unknown yet. Among 12 different COVID-19 targets studied here, the RNA dependent RNA polymerase (RdRp) with RNA and Helicase NCB site show the strongest affinity to Ivermectin amounting -10.4 kcal/mol and -9.6 kcal/mol, respectively. Molecular dynamics of corresponding protein-drug complexes reveals that the drug bound state of RdRp with RNA has better structural stability than the Helicase NCB site, with MM/PBSA free energy of -135.2 kJ/mol, almost twice that of Helicase (-76.6 kJ/mol). The selectivity of Ivermectin to RdRp is triggered by a cooperative interaction of RNA-RdRp by ternary complex formation. Identification of the target and its interaction profile with Ivermectin can lead to more powerful drug designs for COVID-19 and experimental exploration. </p>

Equilibrium Studies of Binary and Ternary Complexes of Palladium(II) Involving Amino Acids

1993 ◽  
Vol 58 (5) ◽  
pp. 1103-1108 ◽  
Author(s):  
Mohamed M. Shoukry ◽  
Eman M. Shoukry
Keyword(s):  
Amino Acids ◽  
Relative Stability ◽  
Ternary Complex ◽  
Formation Constants ◽  
Ternary Complexes ◽  
Conductivity Measurements ◽  
Equilibrium Studies ◽  
Binary And Ternary Complexes ◽  
Binary Complexes

The formation constants of the binary and ternary complexes of palladium(II) with diethylenetriamine and amino acids as ligands have been determined potentiometrically at 25 °C in 0.1 M NaNO3 solution. The relative stability of each ternary complex was compared with that of the corresponding binary complexes in terms of ∆logK values. The mode of chelation was ascertained by conductivity measurements.

scholarly journals The acute transcriptional responses to dietary methionine restriction are triggered by inhibition of ternary complex formation and linked to Erk1/2, mTOR, and ATF4

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kirsten P. Stone ◽  
Sujoy Ghosh ◽  
Jean Paul Kovalik ◽  
Manda Orgeron ◽  
Desiree Wanders ◽  
...  
Keyword(s):  
Stress Response ◽  
Complex Formation ◽  
Ternary Complex ◽  
Target Genes ◽  
Bioinformatic Analysis ◽  
Transcriptional Responses ◽  
Metabolomics Data ◽  
Ternary Complex Formation ◽  
Methionine Restriction

AbstractThe initial sensing of dietary methionine restriction (MR) occurs in the liver where it activates an integrated stress response (ISR) that quickly reduces methionine utilization. The ISR program is regulated in part by ATF4, but ATF4’s prototypical upstream regulator, eIF2α, is not acutely activated by MR. Bioinformatic analysis of RNAseq and metabolomics data from liver samples harvested 3 h and 6 h after initiating MR shows that general translation is inhibited at the level of ternary complex formation by an acute 50% reduction of hepatic methionine that limits formation of initiator methionine tRNA. The resulting ISR is induced by selective expression of ATF4 target genes that mediate adaptation to reduced methionine intake and return hepatic methionine to control levels within 4 days of starting the diet. Complementary in vitro experiments in HepG2 cells after knockdown of ATF4, or inhibition of mTOR or Erk1/2 support the conclusion that the early induction of genes by MR is partially dependent on ATF4 and regulated by both mTOR and Erk1/2. Taken together, these data show that initiation of dietary MR induces an mTOR- and Erk1/2-dependent stress response that is linked to ATF4 by the sharp, initial drop in hepatic methionine and resulting repression of translation pre-initiation.

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