Rational design of diflunisal analogues with reduced affinity for human serum albumin

Spectroscopic and Computational pH Study of NiII and PdII Pyrrole-Imine Chelates with Human Serum Albumin

Human serum albumin (HSA) efficiently transports drugs in vivo: most are organic. Therefore, it is important to delineate the binding of small molecules to HSA. Here, for the first time, we show that HSA binding depends not only on the identity of the d8 metal ion, NiII or PdII, of their complexes with bis(pyrrole-imine), H2PrPyrr, but on the pH level as well. Fluorescence quenching data for native and probe-bound HSA showed that sites close to Trp-214 (subdomain IIA) are targeted. The affinity constants, Ka, ranged from ~3.5 × 103 M-1 to ~1 × 106 M-1 at 37 °C, following the order Pd(PrPyrr) > Ni(PrPyrr) at pH levels of 4 and 7; but Ni(PrPyrr) > Pd(PrPyrr) at a pH level of 9. Ligand uptake is enthalpically driven, dependent mainly on London dispersion forces. The induced CD spectra for the protein-bound ligands could be simulated by hybrid QM:MM TD-DFT methods, allowing us to delineate the binding site of the ligands and to prove that the metal chelates neither decompose nor demetallate after uptake by HSA. The transport and delivery of the metal chelates by HSA in vivo is therefore feasible.

IDL-PPBopt: A Strategy for Prediction and Optimization of Human Plasma Protein Binding of Compounds via an Interpretable Deep Learning Method

The prediction and optimization of pharmacokinetic properties are essential in lead optimization. Traditional strategies mainly depend on the empirical chemical rules from medicinal chemists. However, with the rising amount of data, it is getting more difficult to manually extract useful medicinal chemistry knowledge. To this end, we introduced IDL-PPBopt, a computational strategy for predicting and optimizing the plasma protein binding (PPB) property based on an interpretable deep learning method. At first, a curated PPB data set was used to construct an interpretable deep learning model, which showed excellent predictive performance with a root mean squared error of 0.112 for the entire test set. Then, we designed a detection protocol based on the model and Wilcoxon test to identify the PPB-related substructures (named privileged substructures, PSubs) for each molecule. In total, 22 general privileged substructures (GPSubs) were identified, which shared some common features such as nitrogen-containing groups, diamines with two carbon units, and azetidine. Furthermore, a series of second-level chemical rules for each GPSub were derived through a statistical test and then summarized into substructure pairs. We demonstrated that these substructure pairs were equally applicable outside the training set and accordingly customized the structural modification schemes for each GPSub, which provided alternatives for the optimization of the PPB property. Therefore, IDL-PPBopt provides a promising scheme for the prediction and optimization of the PPB property and would be helpful for lead optimization of other pharmacokinetic properties.

Adenosine Deaminase 1 Overexpression Enhances the Antitumor Efficacy of Chimeric Antigen Receptor-Engineered T Cells

Chimeric antigen receptor (CAR) T cell therapy mediates unprecedented benefit in certain leukemias and lymphomas, but has yet to achieve similar success in combating solid tumors. A substantial body of work indicates that the accumulation of adenosine in the solid tumor microenvironment (TME) plays a crucial role in abrogating immunotherapies. Adenosine deaminase 1 (ADA) catabolizes adenosine into inosine and is indispensable for a functional immune system. We have, for the first time, engineered CAR T cells to overexpress ADA. To potentially improve the pharmacokinetic profile of ADA, we have modified the overexpressed ADA in two ways, through the incorporation of a (1) albumin-binding domain or (2) collagen-binding domain. ADA and modified ADA were successfully expressed by CAR T cells and augmented CAR T cell exhaustion resistance. In a preclinical engineered ovarian carcinoma xenograft model, ADA and collagen-binding ADA overexpression significantly enhanced CAR T cell expansion, tumor tissue infiltration, tumor growth control, and overall survival, whereas albumin-binding ADA overexpression did not. Furthermore, in a syngeneic colon cancer solid tumor model, the overexpression of mouse ADA by cancer cells significantly reduced tumor burden and remodeled the TME to favor antitumor immunity. The overexpression of ADA for enhanced cell therapy is a safe, straightforward, reproducible genetic modification that can be utilized in current CAR T cell constructs to result in an armored CAR T product with superior therapeutic potential.

Part-II- in silico drug design: application and success

In silico tools have indeed reframed the steps involved in traditional drug discovery and development process and the term in silico has become a familiar term in pharmaceutical sector like the terms in vitro and in vivo. The successful design of HIV protease inhibitors, Saquinavir, Indinavir and other important medicinal agents, initiated interest of researchers in structure based drug design approaches (SBDD). The interactions between biomolecules and a ligand, binding energy, free energy and stability of biomolecule-ligand complex can be envisioned and predicted by applying molecular docking studies. Protein-ligand, protein-protein, DNA-ligand interactions etc. aid in elucidating molecular level mechanisms of drug molecules. In the Ligand based drug design (LBDD) approaches, QSAR studies have tremendously contributed to the development of antimicrobial, anticancer, antimalarial agents. In the recent years, multiQSAR (mt-QSAR) approaches have been successfully employed for designing drugs against multifactorial diseases. Output of a research in several instances is rewarding when both SBDD and LBDD approaches are combined. Application of in silico studies for prediction of pharmacokinetics was once a real challenge but one can see unlimited number publications comprising tools, data bases which can accurately predict almost all the pharmacokinetic parameters. Absorption, distribution, metabolism, transporters, blood brain barrier permeability, hERG toxicity, P-gp affinity and several toxicological end points can be accurately predicted for a candidate molecule before its synthesis. In silico approaches are greatly encouraged a result of growing limitations and new legislations related to the animal use for research. The combined use of in vitro data and in silico tools will definitely decrease the use of animal testing in the future.In this chapter, in silico approaches and their applications are reviewed and discussed giving suitable examples.

Spectroscopic Studies of Quinobenzothiazine Derivative in Terms of the In Vitro Interaction with Selected Human Plasma Proteins. Part 1

Plasma proteins play a fundamental role in living organisms. They participate in the transport of endogenous and exogenous substances, especially drugs. 5-alkyl-12(H)-quino[3,4-b][1,4]benzothiazinium salts, have been synthesized as potential anticancer substances used for cancer treatment. Most anticancer substances generate a toxic effect on the human body. In order to check the toxicity and therapeutic dosage of these chemicals, the study of ligand binding to plasma proteins is very relevant. The present work presents the first comparative analysis of the binding of one of the 5-alkyl-12(H)-quino[3,4-b][1,4]benzothiazinium derivatives (Salt1) with human serum albumin (HSA), α-1-acid glycoprotein (AGP) and human gamma globulin (HGG), assessed using fluorescence, UV-Vis and CD spectroscopy. In order to mimic in vivo ligand-protein binding, control normal serum (CNS) was used. Based on the obtained data, the Salt1 binding sites in the tertiary structure of all plasma proteins and control normal serum were identified. Both the association constants (Ka) and the number of binding site classes (n) were calculated using the Klotz method. The strongest complex formed was Salt1-AGPcomplex (Ka = 7.35·104 and 7.86·104 mol·L-1 at excitation wavelengths λex of 275 and 295 nm, respectively). Lower values were obtained for Salt1-HSAcomplex (Ka = 2.45·104 and 2.71·104 mol·L-1) and Salt1-HGGcomplex (Ka = 1.41·104 and 1.33·104 mol·L-1) at excitation wavelengths λex of 275 and 295 nm, respectively, which is a positive phenomenon and contributes to the prolonged action of the drug. Salt1 probably binds to the HSA molecule in Sudlow sites I and II; for the remaining plasma proteins studied, only one binding site was observed. Moreover, using circular dichroism (CD), fluorescence and UV-Vis spectroscopy, no effect on the secondary and tertiary structures of proteins in the absence or presence of Salt1 has been demonstrated. Despite the fact that the conducted studies are basic, from the scientific point of view they are novel and encourage further in vitro and in vivo investigations. As a next part of the study (Part 2), the second new synthetized quinobenzothiazine derivative (Salt2) will be analyzed and published.

Structural Basis of Drug Recognition by Human Serum Albumin

Background:

Human serum albumin (HSA), the most abundant protein in plasma, is a monomeric multi-domain macromolecule with at least nine binding sites for endogenous and exogenous ligands. HSA displays an extraordinary ligand binding capacity as a depot and carrier for many compounds including most acidic drugs. Consequently, HSA has the potential to influence the pharmacokinetics and pharmacodynamics of drugs.

Objective:

In this review, the structural determinants of drug binding to the multiple sites of HSA are analyzed and discussed in detail. Moreover, insight into the allosteric and competitive mechanisms underpinning drug recognition, delivery, and efficacy are analyzed and discussed.

Conclusion:

As several factors can modulate drug binding to HSA (e.g., concurrent administration of drugs competing for the same binding site, ligand binding to allosteric-coupled clefts, genetic inherited diseases, and post-translational modifications), ligand binding to HSA is relevant not only under physiological conditions, but also in the pharmacological therapy management.

Study on the interaction of ertugliflozin with human serum albumin in vitro by multispectroscopic methods, molecular docking, and molecular dynamics simulation

Ertugliflozin is a potent and selective inhibitor of sodium-dependent glucose cotransporters 2 (SGLT2) and used as a monotherapy to improve glycemic control in adult patients with type 2 diabetes. In this study, ertugliflozin binding to human serum albumin (HSA) was investigated by multispectroscopic and computer simulations. The fluorescence spectra demonstrated that the quenching mechanism of ertugliflozin and HSA was static quenching. Thermodynamic parameters indicated that hydrogen bonding and van der Waals forces played a key role in the binding. Fluorescence competition experiments and molecular docking revealed that ertugliflozin bound to HSA sites II. In three-dimensional fluorescence, circular dichroism spectroscopy, and molecular dynamics simulation, ertugliflozin did not affect the basic skeleton structure of HSA but slightly increased the α-helical structure content and changed the microenvironment around amino acid residues. Results provide valuable information on the basis of the interaction of ertugliflozin with HSA.

Photogeneration of Quinone Methides as Latent Electrophiles for Lysine Targeting

Latent electrophiles are nowadays very attractive chemical entities for drug discovery, as they are unreactive unless activated upon binding with the specific target. In this work, the utility of 4-trifluoromethyl phenols as precursors of latent electrophiles, quinone methides (QM), for lysine-targeting is demonstrated. These Michael acceptors were photogenerated for specific covalent modification of lysine residues using human serum albumin (HSA) as a model target. The reactive QM-type intermediates I or II, generated upon irradiation of 4-trifluoromethyl-1-naphthol (1)@HSA or 4-(4-trifluorometylphenyl)phenol (2)@HSA complexes, exhibited chemoselective reactivity toward lysine residues leading to amide adducts, which was confirmed by proteomic analysis. For ligand 1, the covalent modification of residues Lys106 and Lys414 (located in subdomains IA and IIIA, respectively) was observed, whereas for ligand 2, the modification of Lys195 (in subdomain IIA) took place. Docking and molecular dynamics simulation studies provided an insight into the molecular basis of the selectivity of 1 and 2 for these HSA subdomains and the covalent modification mechanism. These studies open the opportunity of performing protein silencing by generating reactive ligands under very mild conditions (irradiation) for specific covalent modification of hidden lysine residues.

A fluorescence probe acted on Site I binding for Human Serum Albumin

A sensitive turn-on probe XYQ, has been developed for the monitoring of HSA species with highly selective and instantaneous response to real- urine sample and living cells imaging. Furthermore, the fluorescence probe acted on Site I and discrimination of HSA from BSA.

Investigating the affinity of BDE154 and 3OH-BDE154 with HSA: Experimental and simulation validation

The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2',4,4', 5,6'-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV-visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure. At pH 7.4, the binding constants of the complexes for site I were relatively comparable and increased in the order BDE154<3OH-BDE154. Then, the secondary structure and kinetic parameters of albumin were analyzed using the circular dichroism spectra and GROMACS software. The data obtained from these simulations indicate that hydrophobic attraction might be the key factor for the stability of complexes. The docking experiments provided further insight into the hydrophobic pocket and showed that 3OH-BDE154 has a stronger binding affinity to human serum albumin than BDE154. The experimental spectral data were obtained and compared with the simulation results, showing good agreement. A detailed analysis of PBDEs-HSA interactions would provide valuable information to better understand the interaction on this class of compounds.

A novel Pd(ii) CNO pincer complex of MR (methyl red): synthesis, crystal structure, interaction with human serum albumin (HSA) in vitro and molecular docking

The C–H activation of methyl red (MR) (MR = 2-{[4-(dimethylamino)phenyl]diazenyl}benzoic acid) was achieved by reaction with Pd(OAc)₂under mild conditions.

Mcl-1 inhibitors: a patent review

INTRODUCTION

The myeloid cell leukemia-1 (MCL-1) protein is one of the key anti-apoptotic members of the B-cell lymphoma-2 (BCL-2) protein family. Over-expression of MCL-1 has been closely related to tumor progression as well as to resistance, not only to traditional chemotherapies but also to targeted therapeutics including BCL-2 inhibitors such as ABT-263. Therefore, there has been extensive research and development in the last decade in both academic and industrial settings to address this unmet medical need. Areas covered: This review covers the research and patent literature of the past 10 years in the field of discovery and development of small-molecule inhibitors of the MCL-1 anti-apoptotic protein. Expert opinion: Small-molecule strategies to disrupt the protein-protein interactions between MCL-1 and its pro-apoptotic counterparts, such as BAK and BIM, have recently emerged. Several small-molecules based on different scaffolds describe promising in vitro data as MCL-1 selective inhibitors. While many lead compounds remain at the in vitro preclinical development stage, the two most recent patent applications describe promising in vivo data, and one small molecule inhibitor has recently entered into clinical development. It is such an exciting moment that the long awaited clinical studies will generate some insight into the therapeutic potential of this anti-cancer approach, and possibly facilitate the further development of other early stage inhibitors.

A Rapid and Quantitative Fluorimetric Method for Protein-Targeting Small Molecule Drug Screening

We demonstrate a new drug screening method for determining the binding affinity of small drug molecules to a target protein by forming fluorescent gold nanoclusters (Au NCs) within the drug-loaded protein, based on the differential fluorescence signal emitted by the Au NCs. Albumin proteins such as human serum albumin (HSA) and bovine serum albumin (BSA) are selected as the model proteins. Four small molecular drugs (e.g., ibuprofen, warfarin, phenytoin, and sulfanilamide) of different binding affinities to the albumin proteins are tested. It was found that the formation rate of fluorescent Au NCs inside the drug loaded albumin protein under denaturing conditions (i.e., 60 °C or in the presence of urea) is slower than that formed in the pristine protein (without drugs). Moreover, the fluorescent intensity of the as-formed NCs is found to be inversely correlated to the binding affinities of these drugs to the albumin proteins. Particularly, the higher the drug-protein binding affinity, the slower the rate of Au NCs formation, and thus a lower fluorescence intensity of the resultant Au NCs is observed. The fluorescence intensity of the resultant Au NCs therefore provides a simple measure of the relative binding strength of different drugs tested. This method is also extendable to measure the specific drug-protein binding constant (KD) by simply varying the drug content preloaded in the protein at a fixed protein concentration. The measured results match well with the values obtained using other prestige but more complicated methods.

In vitro, in silico and integrated strategies for the estimation of plasma protein binding. A review

Plasma protein binding (PPB) strongly affects drug distribution and pharmacokinetic behavior with consequences in overall pharmacological action. Extended plasma protein binding may be associated with drug safety issues and several adverse effects, like low clearance, low brain penetration, drug-drug interactions, loss of efficacy, while influencing the fate of enantiomers and diastereoisomers by stereoselective binding within the body. Therefore in holistic drug design approaches, where ADME(T) properties are considered in parallel with target affinity, considerable efforts are focused in early estimation of PPB mainly in regard to human serum albumin (HSA), which is the most abundant and most important plasma protein. The second critical serum protein α1-acid glycoprotein (AGP), although often underscored, plays also an important and complicated role in clinical therapy and thus the last years it has been studied thoroughly too. In the present review, after an overview of the principles of HSA and AGP binding as well as the structure topology of the proteins, the current trends and perspectives in the field of PPB predictions are presented and discussed considering both HSA and AGP binding. Since however for the latter protein systematic studies have started only the last years, the review focuses mainly to HSA. One part of the review highlights the challenge to develop rapid techniques for HSA and AGP binding simulation and their performance in assessment of PPB. The second part focuses on in silico approaches to predict HSA and AGP binding, analyzing and evaluating structure-based and ligand-based methods, as well as combination of both methods in the aim to exploit the different information and overcome the limitations of each individual approach. Ligand-based methods use the Quantitative Structure-Activity Relationships (QSAR) methodology to establish quantitate models for the prediction of binding constants from molecular descriptors, while they provide only indirect information on binding mechanism. Efforts for the establishment of global models, automated workflows and web-based platforms for PPB predictions are presented and discussed. Structure-based methods relying on the crystal structures of drug-protein complexes provide detailed information on the underlying mechanism but are usually restricted to specific compounds. They are useful to identify the specific binding site while they may be important in investigating drug-drug interactions, related to PPB. Moreover, chemometrics or structure-based modeling may be supported by experimental data a promising integrated alternative strategy for ADME(T) properties optimization. In the case of PPB the use of molecular modeling combined with bioanalytical techniques is frequently used for the investigation of AGP binding.

Recent advances in cancer therapeutics

In the past 20 years, cancer therapeutics has undergone a paradigm shift away from the traditional cytotoxic drugs towards the targeting of proteins intimately involved in driving the cancer phenotype. The poster child for this alternative approach to the treatment of cancer is imatinib, a small-molecule kinase inhibitor designed to target chronic myeloid leukaemia driven by the BCR-ABL translocation in a defined patient population. The improvement in survival achieved by treatment of this patient cohort with imatinib is impressive. Thus, the aim is to provide efficacy but with low toxicity. The role of the medicinal chemist in oncology drug discovery is now closely aligned with the role in most other therapeutic areas with high-throughput and/or fragment-based screening, structure-based design, selectivity, pharmacokinetic optimisation and pharmacodynamic biomarker modulation, all playing a familiar part in the process. In this chapter, we selected four areas in which compounds are either approved drugs or in clinical trials. These are chaperone inhibitors, kinase inhibitors, histone deacetylase inhibitors and inhibitors of protein-protein interactions. Even within these areas, we have been selective, particularly for kinase inhibitors, and our aim has been to exemplify newer approaches and novel aspects of medicinal chemistry.

Tuning transthyretin amyloidosis inhibition properties of iododiflunisal by combinatorial engineering of the nonsalicylic ring substitutions

Two series of iododiflunisal and diflunisal analogues have been obtained by using a two step sequential reaction solution-phase parallel synthesis. The synthesis combined an aqueous Suzuki-Miyaura cross-coupling and a mild electrophilic aromatic iodination step using a new polymer-supported iodonium version of Barluenga's reagent. From a selected set of 77 noniodinated and 77 iodinated diflunisal analogues, a subset of good transthyretin amyloid inhibitors has been obtained with improved turbidimetry inhibition constants, high binding affinity to transthyretin, and good selectivity for TTR compared to other thyroxine binding proteins.

Quantum molecular modelling of ibuprofen bound to human serum albumin

The total interaction energies of the ibuprofen complexed with FA3/FA4 and FA6 binding sites of human serum albumin are in agreement with the hypothesis that the Sudlow's site II is the main binding pocket for ibuprofen.

Interactive association of drugs binding to human serum albumin

Human serum albumin (HSA) is an abundant plasma protein, which attracts great interest in the pharmaceutical industry since it can bind a remarkable variety of drugs impacting their delivery and efficacy and ultimately altering the drug’s pharmacokinetic and pharmacodynamic properties. Additionally, HSA is widely used in clinical settings as a drug delivery system due to its potential for improving targeting while decreasing the side effects of drugs. It is thus of great importance from the viewpoint of pharmaceutical sciences to clarify the structure, function, and properties of HSA–drug complexes. This review will succinctly outline the properties of binding site of drugs in IIA subdomain within the structure of HSA. We will also give an overview on the binding characterization of interactive association of drugs to human serum albumin that may potentially lead to significant clinical applications.

Discovery of ABT-263, a Bcl-family protein inhibitor: observations on targeting a large protein-protein interaction

BACKGROUND

The discovery of ABT-263, a rationally designed Bcl-2/Bcl-xL inhibitor at present in Phase I clinical trials for cancer, is described. Emphasis is placed on the specific hurdles overcome throughout the discovery process that relate to the nature of the targeted protein-protein interaction (PPI).

OBJECTIVE/METHODS

This review draws on observations from the experience of discovering ABT-263 and discusses them within the framework of the larger issue of discovering drugs targeting PPIs. Issues discussed include the 'hot spot' paradigm, hit and lead generation, serum protein binding, structure-based design, and in particular, hydrophobicity and molecular size and their relation to pharmacokinetic/pharmacodynamic properties.

RESULTS/CONCLUSION

Approaches to understanding obstacles thought of as being specifically attached to PPIs, and existing techniques to combat these obstacles, were very helpful in overcoming them. The example of ABT-263 provides evidence that the larger family of PPI targets is more tractable than may have been thought.

The importance of plasma protein binding in drug discovery

Plasma protein binding of drugs is a well-recognised phenomena, but it is only recently that the implications for drug action in vivo have been fully appreciated. Plasma proteins, by virtue of their high concentration, control the free drug concentration in plasma and in compartments in equilibrium with plasma, thereby, effectively attenuating drug potency in vivo. The historical background and thermodynamic basis for the 'Free Drug Principle' is presented, along with special considerations for intracellular targets, deep compartments and α1-acid glycoprotein binding. Real and apparent exceptions to the principle are discussed along with a survey of citations from the recent medicinal chemistry literature.

Utility of protein structures in overcoming ADMET-related issues of drug-like compounds

The number of solved X-ray structures of proteins relevant for ADMET processes of drug molecules has increased remarkably over recent years. In principle, this development offers the possibility to complement the quantitative structure-property relationship (QSPR)-dominated repertoire of in silico ADMET methods with protein-structure-based approaches. However, the complex nature and the weak nonspecific ligand-binding properties of ADMET proteins take structural biology methods and current docking programs to the limit. In this review we discuss the utility of protein-structure-based design and docking approaches aimed at overcoming issues related to plasma protein binding, active transport via P-glycoprotein, hERG channel mediated cardiotoxicity and cytochrome P450 inhibition, metabolism and induction.

Lessons from the crystallographic analysis of small molecule binding to human serum albumin

SUMMARY

Human serum albumin (HSA) is an abundant and highly soluble plasma protein with the capacity to bind a remarkably diverse set of lipophilic anionic compounds so that it fulfils important roles in the transport of nutrients, hormones and toxins. The protein attracts great interest from the pharmaceutical industry since it can also bind a variety of drug molecules, impacting their delivery and efficacy. Our understanding of the binding and transport properties of albumin has been transformed by structural studies of the protein, in which crystallographic analysis has played a leading role. This review summarises the main insights to have accrued from this work, highlighting the significant advances that have been made but also pointing out some of the challenges ahead. Since further progress is likely to benefit from increased structural scrutiny of HSA, methodological developments instrumental to the success of crystallographic analysis of the protein are discussed in some detail.