Dissociation Constant For Binding Research Articles

Elucidating nonlinear pharmacokinetics of telmisartan: Integration of target-mediated drug disposition and OATP1B3-mediated hepatic uptake in a physiologically based model.

Telmisartan, a selective inhibitor of angiotensin II receptor type 1 (AT1), demonstrates nonlinear pharmacokinetics (PK) when orally administered in ascending doses to healthy volunteers, but the underlying mechanisms remain unclear. This study presents a physiologically based pharmacokinetic model integrated with target-mediated drug disposition (TMDD-PBPK model) to explore the mechanism of its nonlinear PK. We employed the Cluster-Gauss Newton method for top-down analysis, estimating the invivo Km,OATP1B3 (Michaelis-Menten constant for telmisartan hepatic uptake via Organic Anion Transporting Polypeptide 1B3) to be 2.0-5.7 nM. This range is significantly lower than the reported invitro value of 810 nM, obtained in 0.3% human serum albumin (HSA) conditions. Further validation was achieved through invitro assessment in plated human hepatocytes with 4.5% HSA, showing a Km of 4.5 nM. These results underscore the importance of albumin-mediated uptake effect for the hepatic uptake of telmisartan. Our TMDD-PBPK model, developed through a "middle-out" approach, underwent sensitivity analysis to identify key factors in the nonlinear PK of telmisartan. We found that the nonlinearity in the area under the concentration-time curve (AUC) and/or maximum concentration (Cmax) of telmisartan is sensitive to Km,OATP1B3 across all dosages. Additionally, the dissociation constant (Kd) for telmisartan binding to the AT1 receptor, along with its receptor abundance, notably influences PK at lower doses (below 20 mg). In conclusion, the nonlinear PK of telmisartan appears primarily driven by hepatic uptake saturation across all dose ranges and by AT1-receptor binding saturation, notably at lower doses.

Calculating Binding Free Energies in Model Host-Guest Systems with Unrestrained Advanced Sampling.

Host-guest interactions are important to the design of pharmaceuticals and, more broadly, to soft materials as they can enable targeted, strong, and specific interactions between molecules. The binding process between the host and guest may be classified as a "rare event" when viewing the system at atomic scales, such as those explored in molecular dynamics simulations. To obtain equilibrium binding conformations and dissociation constants from these simulations, it is essential to resolve these rare events. Advanced sampling methods such as the adaptive biasing force (ABF) promote the occurrence of less probable configurations in a system, therefore facilitating the sampling of essential collective variables that characterize the host-guest interactions. Here, we present the application of ABF to a rod-cavitand coarse-grained model of host-guest systems to acquire the potential of mean force. We show that the employment of ABF enables the computation of the configurational and thermodynamic properties of bound and unbound states, including the free energy landscape. Moreover, we identify important dynamic bottlenecks that limit sampling and discuss how these may be addressed in more general systems.

Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies.

Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.

Plant-Produced Therapeutic Crizanlizumab Monoclonal Antibody Binds P-Selectin to Alleviate Vaso-occlusive Pain Crises in Sickle Cell Disease.

Sickle Cell Disease (SCD) is a severe genetic disorder causing vascular occlusion and pain by upregulating the adhesion molecule P-selectin on endothelial cells and platelets. It primarily affects infants and children, causing chronic pain, circulatory problems, organ damage, and complications. Thus, effective treatment and management are crucial to reduce SCD-related risks. Anti-P-selectin antibody Crizanlizumab (Crimab) has been used to treat SCD. In this study, the heavy and light chain (HC and LC) genes of anti-P-Selectin antibody Crimab were cloned into a plant expression binary vector. The HC gene was under control of the duplicated 35S promoter and nopaline synthase (NOS) terminator, whereas the LC gene was under control of the potato proteinase inhibitor II (PIN2) promoter and PIN2 terminator. Agrobacterium tumefaciens LBA4404 was used to transfer the genes into the tobacco (Nicotiana tabacum cv. Xanthi) plant. In plants the genomic PCR and western blot confirmed gene presence and expression of HC and LC Crimab proteins in the plant, respectively. Crimab was successfully purified from transgenic plant leaf using protein A affinity chromatography. In ELISA, plant-derived Crimab (CrimabP) had similar binding activity to P-selectin compared to mammalian-derived Crimab (CrimabM). In surface plasmon resonance, the KD (dissociation binding constant) and response unit values were lower and higher than CrimabP, respectively. Taken together, these results demonstrate that the transgenic plant can be applied to produce biofunctional therapeutic monoclonal antibody.

Substitution of Glu378 in EF-Tu disrupts binding to KKL-55.

Trans -translation is a target for the development of new antibiotics. The potential antibiotic lead compound KKL-55 binds to EF-Tu and inhibits trans -translation. Previous structural and biochemical studies showed that glutamate 378 in EF-Tu directly contacts bound KKL-55, but mutation of residue 378 to alanine had no effect on the equilibrium dissociation constant for binding of EF-Tu and KKL-55. Here, we found that a variant of EF-Tu with tryptophan at position 378 increases the K d for binding of EF-Tu and KKL-55 by >6-fold, indicating that a larger side chain at this position is disruptive. The E378W variant decreased the amount of translation in vitro and no trans -translation could be detected with this variant. These data provide further evidence that residue 378 of EF-Tu forms part of the KKL-55 binding pocket and are consistent with a lack of spontaneous mutants resistant to KKL-55.

Engineering minimal tissue inhibitors of metalloproteinase targeting MMPs via gene shuffling and yeast surface display.

Overexpression of specific matrix metalloproteinases (MMPs) has a key role in development of several diseases, such as cancer, neurological disorders, and cardiovascular diseases due to their critical role in degradation and remodeling of the extracellular matrix (ECM). Tissue inhibitors of metalloproteinases (TIMPs), a family of four in humans, are endogenous inhibitors of MMPs. TIMPs have a high level of sequence and structure homology, with a broad range of binding and inhibition to the family of MMPs. It is important to identify the key motifs of TIMPs responsible for inhibition of MMPs to developefficient therapeutics targeting specific MMPs. We used DNA shuffling between the human TIMP family to generate a minimal TIMP hybrid library in yeast to identify the dominant minimal MMP inhibitory regions. The minimal TIMP variants screened toward MMP-3 and MMP-9 using fluorescent-activated cell sorting (FACS). Interestingly, several minimal TIMP variants selected after screening toward MMP-3cd or MMP-9cd, with lengths as short as 20 amino acids, maintained or improved binding to MMP-3 and MMP-9. The TIMP-MMP binding dissociation constant (KD ), in the nM range, and MMP inhibition constants (Ki ), in the pM range, of these minimal TIMP variants were similar to the N-terminal domain of TIMP-1 on the yeast surface and in solution indicating the potency of these minimal variants as MMP inhibitors. We further used molecular modeling simulation, and molecular docking of the minimal TIMP variants in complex with MMP-3cd to understand the binding and inhibition mechanism of these variants.

ARL15, a GTPase implicated in rheumatoid arthritis, potentially repositions its truncated N-terminus as a function of guanine nucleotide binding

The ADP ribosylation factor like protein 15 (ARL15) gene encodes for an uncharacterized GTPase associated with rheumatoid arthritis (RA) and other metabolic disorders. Investigation of the structural and functional attributes of ARL15 is important to position the protein as a potential drug target. Using spectroscopy, we demonstrated that ARL15 exhibits properties inherent of GTPases. The Km and Vmax of the enzyme were calculated to be 100 μM and 1.47 μmole/min/μL, respectively. The equilibrium dissociation constant (Kd) of GTP binding with ARL15 was estimated to be about eight-fold higher than that of GDP. Small Angle X-ray Scattering (SAXS) data indicated that in solution, the apo state of monomeric ARL15 adopts a shape characterized by a globe of maximum linear dimension (Dmax) of 6.1 nm, and upon binding to GTP or GDP, the vector distribution profile changes to peak-n-tail shoulder with Dmax extended to 7.6 and 7.7 nm, respectively. Structure restoration using a sequence-based template and experimental SAXS data provided the first visual insight revealing that the folded N-terminal in the unbound state of the protein may toggle open upon binding to guanine nucleotides. The conformational dynamics observed in the N-terminal region offer a scope to develop drugs that target this unique GTPase, potentially providing treatments for a range of metabolic disorders.

Analysis of some flavonoids for inhibitory mechanism against cancer target phosphatidylinositol 3-kinase (PI3K) using computational tool.

Cancer has been one of the leading causes of mortality worldwide over the past few years. Some progress has been made in the development of more effective cancer therapeutics, resulting in improved survival rates. However, the desired outcome in the form of successful treatment is yet to be achieved. There is high demand for the development of innovative, inexpensive, and effective anticancer treatments using natural resources. Natural compounds have been increasingly discovered and used for cancer therapy owing to their high molecular diversity, novel biofunctionality, and minimal side effects. These compounds can be utilized as chemopreventive agents because they can efficiently inhibit cell growth, control cell cycle progression, and block several tumor-promoting signaling pathways. PI3K is an important upstream protein of the PI3K-Akt-mTOR pathway and a well-established cancer therapeutic target. This study aimed to explore the small molecules, natural flavonoids, viz. quercetin, luteolin, kaempferol, genistein, wogonin, daidzein, and flavopiridol for PI3Kγ kinase activity inhibition. In this study, the binding pose, interacting residues, molecular interactions, binding energies, and dissociation constants were investigated. Our results showed that these flavonoids bound well with PI3Kγ with adequate binding strength scores and binding energy ranging from (-8.19 to -8.97Kcal/mol). Among the explored ligands, flavopiridol showed the highest binding energy of -8.97Kcal/mol, dock score (-44.40), and dissociation constant term, of 6.58 against PI3Kγ. Based on the above results, the stability of the most promising ligand, flavopiridol, against PI3Kγ was evaluated by molecular dynamics simulations for 200ns, confirming the stable flavopiridol and PI3Kγ complex. Our study suggests that among the selected flavonoids specifically flavopiridol may act as potential inhibitors of PI3Kγ and could be a therapeutic alternative to inhibit the PI3Kγ pathway, providing new insights into rational drug discovery research for cancer therapy.

A green one-pot synthetic protocol of hexahydropyrimido[4,5-d]pyrimidin-4(1H)-one derivatives: molecular docking, ADMET, anticancer and antimicrobial studies.

Ten hexahydropyrimido[4,5-d]pyrimidine derivatives have been synthesized by using a green and time-efficient microwave method. The synthesized motifs were evaluated for their anticancer activity, antimicrobial activity, molecular docking, drug likeliness and ADMET studies. Comparatively, the hetero-aromatic pyrazole substituted compound 4a exhibited the highest anticancer activity [Mean growth percent: 35.57], while EDG [-N(CH3)2] substituted compound 4i indicated very good activity [Mean growth percent: 60.92] against various cell lines. From the computational studies, Compound 4a passed the drug-likeness and ADME properties, fewer toxic properties, and potent inhibitory potential against the RIPK2 with significant binding affinity. In-silico molecular docking revealed that the compound 4a has significant binding energy (-9.8kcal/mol) and dissociation constant (0.54µM) properties. Additionally, synthesized motifs were evaluated for antimicrobial activity by MIC referencing the standards. According to the SAR evaluations, the compounds 4f (4-NO2), 4g (3-NO2), and 4h (2-Cl) that include EWGs substituted aldehydes performed well as antimicrobials against selected bacterial and fungal strains. Thus, the synthesized pyrimido[4,5-d]pyrimidine with the heterocyclic and EWGs substituents could act as a potential candidate after further structural optimization for anticancer and antimicrobial drug discovery, respectively.

Plant Regulation Functions of Novel Phthalimide Compounds Based on AtPYL2.

Novel agents contain the structure of phthalimide, which has antibacterial, insecticidal, and herbicidal activities. Recently, studies reported that these compounds can bind to plant hormone receptors and play important regulatory roles. In this study, the functions of agents were studied with in vitro and in vivo assays. The abscisic acid (ABA) receptor pyrabactin resistant-like 2 (PYL2) protein in Arabidopsis thaliana was expressed, purified, and crystallized; the analysis results of the crystal structure showed three AtPYL2 subunits in each asymmetric unit. The affinity of compounds Z1-Z11 to the AtPYL2 protein was tested by microscale thermophoresis (MST) and then verified by isothermal titration calorimetry (ITC). Furthermore, the binding pockets were found using molecular docking to verify the target relationships. Relevant in vivo assays for seed germination and a root growth assay were conducted, with the plant samples being treated with target compounds. The results show that the compounds Z3, Z5, and Z10 target AtPYL2 and that the dissociation constants for binding by MST were 3.59, 3.54, and 3.97 μmol/L, respectively, among them, and the molecular docking results showed that compounds Z3, Z5, and Z10 formed hydrophobic interactions with amino acid residues through hydrogen or halogen bonding. This highlights their potential as an ABA receptor protein agonist. On the other hand, in vivo, compounds Z3, Z5, and Z10 had different inhibitory effects on seed germination, with compound Z5 inhibiting the root growth of A. thaliana and compound Z10 affecting root growth. In conclusion, these compounds could regulate plant growth and could be further developed as new plant-regulating agents.

Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis

One strategy to combat antimicrobial resistance is the discovery of new classes of antibiotics. Most antibiotics will at some point interact with the bacterial membrane to either interfere with its integrity or to cross it. Reliable and efficient tools for determining the dissociation constant for membrane binding (KD) and the partitioning coefficient between the aqueous- and membrane phases (KP) are therefore important tools for discovering and optimizing antimicrobial hits. Here we demonstrate that microscale thermophoresis (MST) can be used for label-free measurement of KD by utilising the intrinsic fluorescence of tryptophan and thereby removing the need for chromophore labelling. As proof of principle, we have used the method to measure the binding of a set of small cyclic AMPs to large unilamellar vesicles (LUVs) and two types of lipid nanodiscs assembled by styrene maleic acid (SMA) and quaternary ammonium SMA (SMA-QA). The measured KD values correlate well with the corresponding measurements using surface plasmon resonance (SPR), also broadly reflecting the tested AMPs’ minimal inhibition concentration (MIC) towards S. aureus and E. coli. We conclude that MST is a promising method for fast and cost-efficient detection of peptide-lipid interactions or mapping of sample conditions in preparation for more advanced studies that rely on expensive sample preparation, labelling and/or instrument time.

Comprehensive biophysical characterization of AAV-AAVR interaction uncovers serotype- and pH-dependent interaction

After more than two decades of research and development, adeno-associated virus (AAV) has become one of the dominant delivery vectors in gene therapy. Despite the focused research, the cell entry pathway for AAV is still not fully understood. Universal AAV receptor (AAVR) has been identified to be involved in cellular entry of different AAV serotypes. With the unveiling of the high-resolution AAV-AAVR complex structure by cryogenic electron microscopy, the atomic level interaction between AAV and AAVR has become the focus of study in recent years. However, the serotype dependence of this binding interaction and the effect of pH have not been studied. Here, orthogonal approaches including bio-layer interferometry (BLI), size-exclusion chromatography coupled to multi-angle laser scattering (SEC-MALS) and sedimentation velocity analytical ultracentrifugation (SV-AUC) were utilized to study the interaction between selected AAV serotypes and AAVR under different pH conditions. A robust BLI method was developed and the equilibrium dissociation binding constants (KD) between different AAV serotypes (AAV1, AAV5 and AAV8) and AAVR was measured. The binding constants measured by BLI together with orthogonal methods (SEC-MALS and SV-AUC) all confirmed that AAV5 has the strongest binding affinity followed by AAV1 while AAV8 binds the weakest. It was also observed that lower pH promotes the binding between AAV and AAVR and neutral or slightly basic conditions lead to very weak binding. These data indicate that for certain serotypes, AAVR may play a prominent role in trafficking AAV to the Golgi rather than acting as a host cell receptor. Information obtained from these combinatorial biophysical methods can be used to engineer future generations of AAVs to have better transduction efficiency.

Construction and Preclinical Evaluation of a 124/125I-Labeled Specific Antibody Targeting PD-L2 in Lung Cancer

Programmed cell death-ligand 2 (PD-L2) is an important emerging molecule of the immune checkpoint, which is closely related to the prognosis of patients with immune checkpoint inhibitor (ICI) therapy. The quantification of PD-L2 can provide a potential reference for patients who benefit from ICI treatment. In this study, we used iodine isotope (nat/124/125I)-labeled PD-L2 antibody (ATL2) to noninvasively detect PD-L2 expression in mice with human lung adenocarcinoma A549 cell lines. The radiochemical yields of 125I-ATL2 and 124I-ATL2 were 73.56 ± 3.72% and 69.46 ± 2.05%, respectively. The radiochemical purity (RCP) of the tracers was more than 99%. The positive cell line A549-PDL2 was constructed by lentivirus. Western blot, immunofluorescence, and flow cytometry indicated that the A549-PDL2 cells showed a higher PD-L2 protein level than the A549 cells. The dissociation constant of 125I-ATL2 binding to the PD-L2 protein was 7.25 nM. Cellular uptake experiments confirmed that the uptake of 125I-ATL2 in A549-PDL2 cells was higher than that in A549 cells at each time point (P < 0.0001). Micro-PET/CT showed significant uptake in the tumor region of A549-PDL2 tumor-bearing mice 24 h postinjection of 124I-ATL2 compared with that of other groups (SUVmax = 0.75 ± 0.06, 0.19 ± 0.07, and 0.27 ± 0.05, respectively). Consistently, the biodistribution of the tracers at 24 h postinjection showed a higher tumor uptake in A549-PDL2 mice (7.11 ± 0.38 %ID/g for 124I-ATL2 in A549-PDL2 mice vs 2.72 ± 0.15 %ID/g for 124I-ATL2 in A549 mice vs 3.89 ± 0.65 %ID/g for 124I-IgG in A549-PDL2 mice). The dosimetry estimation by using Olinda software showed that the effective dose of 124I-ATL2 was 3.62 × 10-2 mSv/MBq, which is within the range of acceptable doses. Immunohistochemical results further confirmed that the expression of PD-L2 in the tumor tissues of A549-PDL2-bearing mice was higher than that of the A549 model mice. In conclusion, the development of 124/125I-ATL2 provides the first noninvasive quantification of PD-L2 expression in lung cancer by molecular imaging, which provides a new reference for screening potential beneficiaries of ICI therapy.

An Engineered β-Hairpin Peptide Forming Thermostable Complexes with ZnII , NiII , and CuII through a His3 Site.

The three-dimensional structure of a peptide, which determines its function, can denature at elevated temperatures, in the presence of chaotropic reagents, or in organic solvents. These factors limit the applicability of peptides. Herein, we present an engineered β-hairpin peptide containing a His3 site that forms complexes with ZnII , NiII , and CuII . Circular dichroism spectroscopy shows that the peptide-metal complexes exhibit melting temperatures up to 80 °C and remain folded in 6 M guanidine hydrochloride as well as in organic solvents. Intrinsic fluorescence titration experiments were used to determine the dissociation constants of metal binding in the nano- to sub-nanomolar range. The coordination geometry of the peptide-CuII complex was studied by EPR spectroscopy, and a distorted square planar coordination geometry with weak interactions to axial ligands was revealed. Due to their impressive stability, the presented peptide-metal complexes open up interesting fields of application, such as the development of a new class of peptide-metal catalysts for stereoselective organic synthesis or the directed design of extremophilic β-sheet peptides.

Development of peptide affinity ligands for the purification of polyclonal and monoclonal Fabs from recombinant fluids

Engineered multi-specific monoclonal antibodies (msAbs) and antibody fragments offer valuable therapeutic options against metabolic disorders, aggressive cancers, and viral infections. The advancement in molecular design and recombinant expression of these next-generation drugs, however, is not equaled by the progress in downstream bioprocess technology. The purification of msAbs and fragments requires affinity adsorbents with orthogonal biorecognition of different portions of the antibody structure, namely its Fc (fragment crystallizable) and Fab (fragment antigen-binding) regions or the CH1-3 and CL chains. Current adsorbents rely on protein ligands that, while featuring high binding capacity and selectivity, need harsh elution conditions and suffer from high cost, limited biochemical stability, and potential release of immunogenic fragments. Responding to these challenges, we undertook the de novo discovery of peptide ligands that target different regions of human Fab and enable product release under mild conditions. The ligands were discovered by screening a focused library of 12-mer peptides against a feedstock comprising human Fab and Chinese hamster ovary host cell proteins (CHO HCPs). The identified ligands were evaluated via binding studies as well as molecular docking simulations, returning excellent values of binding capacity (Qmax ∼ 20 mg of Fab per mL of resin) and dissociation constant (KD = 2.16·10−6 M). Selected ligand FRWNFHRNTFFP and commercial Protein L ligands were further characterized by measuring the dynamic binding capacity (DBC10%) at different residence times (RT) and performing the purification of polyclonal and monoclonal Fabs from CHO-K1 cell culture fluids. The peptide ligand featured DBC10% ∼ 6-16 mg/mL (RT of 2 min) and afforded values of yield (93–96%) and purity (89–96%) comparable to those provided by Protein L resins.

Targeting the HIV-1 Tat and Human Tat Protein Complex through Natural Products: An In Silico Docking and Molecular Dynamics Simulation Approach

Background: Tat protein is considered essential for substantial HIV-1 replication, and is also required to break HIV-1 latency, resulting in productive HIV replication. The multifaceted regulatory role of HIV Tat and the fact that it is expressed in the early stages of HIV infection justify its potential as an anti-HIV drug target. Objective: The present study was undertaken with the aim to target HIV-1 Tat protein with natural compounds which could help in identifying potential inhibitors against HIV-1 Tat. Methods: In this study, we compared the binding of Tat protein and Human P-TEFb Tat protein complex (TPC) with phyto-steroids and terpenes to evaluate their potential for HIV-1 treatment. The docking ability of plant products with HIV-1 Tat and TPC was studied with respect to dissociation constant, geometric shape complementary score, approximate interface area, and binding energy using Patch dock and YASARA. Molecular dynamics simulation was set up to investigate the interactions of the natural compounds with Tat protein and human tat protein complex (TPC). Results: The binding energy and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A with Tat and TPC were comparable to antiretroviral drugs, Maraviroc and Emtricitabine. The natural products, Diosgenin, Ginkgolide A and Catharanthine, showed the highest binding energy and were stable with Tat protein and TPC in the entire MD simulation run. Conclusion: The natural products, Diosgenin, Ginkgolide A and Catharanthine, showed highest binding energy and were stable with Tat protein and TPC in the entire MD simulation run. The binding energy and dissociation constant of Diosgenin, Catharanthine and Ginkgolide A with Tat and TPC were comparable to antiretroviral drugs, Maraviroc and Emtricitabine.

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.

Redox partner adrenodoxin alters cytochrome P450 11B1 ligand binding and inhibition

Human cytochrome P450 11B1 (CYP11B1) generation of the major glucocorticoid cortisol requires two electrons delivered sequentially by the iron‑sulfur protein adrenodoxin. While the expected adrenodoxin binding site is on the opposite side of the heme and 15–20 Å away, evidence is provided that adrenodoxin allosterically impacts CYP11B1 ligand binding and catalysis. The presence of adrenodoxin both decreases the dissociation constant (Kd) for substrate binding and increases the proportion of substrate that is bound at saturation. Adrenodoxin additionally decreases the Michaelis-Menten constant for the native substrate. Similar studies with several inhibitors also demonstrate the ability of adrenodoxin to modulate inhibition (IC50 values). Somewhat similar allosterism has recently been observed for the closely related CYP11B2/aldosterone synthase, but there are several marked differences in adrenodoxin effects on the two CYP11B enzymes. Comparison of the sequences and structures of these two CYP11B enzymes helps identify regions likely responsible for the functional differences. The allosteric effects of adrenodoxin on CYP11B enzymes underscore the importance of considering P450/redox partner interactions when evaluating new inhibitors.

Immunoinformatics-based Identification of Highly Conserved Cytotoxic T-Cell Epitopes in Polyprotein pp220 of African Swine Fever Virus

Background:High mortality rate of pigs peaked in 2020 due to the re-emergence of a deadly African swine fever virus (ASFV) which has led to transcontinental outbreaks in Europe, reportedly from 2014 to 2019, and in Asia and the Pacific from 2018–2020. Given the huge socioeconomic consequences of the disease, vaccines that will prime the immunity of swine against this pathogen is a dire necessity.Methods:Insilicoidentification and characterization of highly conserved cytotoxic T-cell (CD8+) epitopes derived from one of its structural proteins, pp220, were analyzed. Protein sequences of pp220 were retrieved and clustered to obtain highly conserved sequences. Cross-reactive epitopes were filtered out, and the remaining epitopes were docked with swine leukocyte antigen-1*0401 (SLA-1*0401). Furthermore, the epitope stability was determined by comparing binding energy, dissociation constant, and eigenvalues of the epitopes with the values of positive control, influenza-epitope complex.Results:This study showed that 20 highly conserved epitopes promiscuously bind to two or more SLAs and 9 of which epitopes (ALDLSLIGF, QIYKTLLEY, FLNKSTQAY, IADAINQEF, IINPSITEY, AINTFMYYY, SLYPTQFDY, RSNPGSFYW, and RLDRKHILM) that were validated exhibit potential immunogenicity based on the acceptable binding energy, dissociation constant, and eigenvalues.Conclusion:This study has identified epitopes that show high conservancy, reducing the chance of epitope immune evasion. It is anticipated that the identified epitopes must be further evaluated as a potential immunotherapeutic agent in developing an epitope-based vaccine against ASFV.

Comparative Reverse Vaccinology of Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa, Frequent Pathogens of Atlantic Salmon and Lumpfish Aquaculture.

Marine finfish aquaculture is affected by diverse infectious diseases, and they commonly occur as co-infection. Some of the most frequent and prevalent Gram-negative bacterial pathogens of the finfish aquaculture include Piscirickettsia salmonis, Aeromonas salmonicida, Yersinia ruckeri, Vibrio anguillarum and Moritella viscosa. To prevent co-infections in aquaculture, polyvalent or universal vaccines would be ideal. Commercial polyvalent vaccines against some of these pathogens are based on whole inactivated microbes and their efficacy is controversial. Identification of common antigens can contribute to the development of effective universal or polyvalent vaccines. In this study, we identified common and unique antigens of P. salmonis, A. salmonicida, Y. ruckeri, V. anguillarum and M. viscosa based on a reverse vaccinology pipeline. We screened the proteome of several strains using complete available genomes and identified a total of 154 potential antigens, 74 of these identified antigens corresponded to secreted proteins, and 80 corresponded to exposed outer membrane proteins (OMPs). Further analysis revealed the outer membrane antigens TonB-dependent siderophore receptor, OMP assembly factor BamA, the LPS assembly protein LptD and secreted antigens flagellar hook assembly protein FlgD and flagellar basal body rod protein FlgG are present in all pathogens used in this study. Sequence and structural alignment of these antigens showed relatively low percentage sequence identity but good structural homology. Common domains harboring several B-cells and T-cell epitopes binding to major histocompatibility (MHC) class I and II were identified. Selected peptides were evaluated for docking with Atlantic salmon (Salmo salar) and Lumpfish MHC class II. Interaction of common peptide-MHC class II showed good in-silico binding affinities and dissociation constants between −10.3 to −6.5 kcal mol−1 and 5.10 × 10−9 to 9.4 × 10−6 M. This study provided the first list of antigens that can be used for the development of polyvalent or universal vaccines against these Gram-negative bacterial pathogens affecting finfish aquaculture.