Discovery pharmaceutics--challenges and opportunities

Intrinsic Solubility of Ionizable Compounds from pKa Shift

Aqueous solubility of pharmaceutical substances plays an important role in small molecule drug discovery and development, with ionizable groups often employed to enhance solubility. Drug candidate compounds often contain ionizable groups to increase their solubility. Recognizing that the electrostatically charged form of the compound is much more soluble than the uncharged form, this work proposes a model to explore the relationship between the pKa shift of the ionizable group and dissolution equilibria. The model considers three forms of a compound: dissolved-charged, dissolved-uncharged, and aggregated-uncharged. It analyzes two linked equilibria: the protonation of the ionizable group and the dissolution-aggregation of the uncharged form, with the observed pKa shift depending on the total concentration of the compound. The active concentration of the aggregates determines this shift. The model was explored through the determination of the pKa shift and intrinsic solubility of specific compounds, such as ICPD47, a high-affinity inhibitor of the Hsp90 chaperone protein and anticancer target, as well as benzoic acid and benzydamine. The model holds the potential for a more nuanced understanding of intrinsic solubility and may lead to advancements in drug discovery and development.

The curse and blessing of abundance-the evolution of drug interaction databases and their impact on drug network analysis

BACKGROUND

Widespread bioinformatics applications such as drug repositioning or drug-drug interaction prediction rely on the recent advances in machine learning, complex network science, and comprehensive drug datasets comprising the latest research results in molecular biology, biochemistry, or pharmacology. The problem is that there is much uncertainty in these drug datasets-we know the drug-drug or drug-target interactions reported in the research papers, but we cannot know if the not reported interactions are absent or yet to be discovered. This uncertainty hampers the accuracy of such bioinformatics applications.

RESULTS

We use complex network statistics tools and simulations of randomly inserted previously unaccounted interactions in drug-drug and drug-target interaction networks-built with data from DrugBank versions released over the plast decade-to investigate whether the abundance of new research data (included in the latest dataset versions) mitigates the uncertainty issue. Our results show that the drug-drug interaction networks built with the latest dataset versions become very dense and, therefore, almost impossible to analyze with conventional complex network methods. On the other hand, for the latest drug database versions, drug-target networks still include much uncertainty; however, the robustness of complex network analysis methods slightly improves.

CONCLUSIONS

Our big data analysis results pinpoint future research directions to improve the quality and practicality of drug databases for bioinformatics applications: benchmarking for drug-target interaction prediction and drug-drug interaction severity standardization.

Drug Repurposing Using Modularity Clustering in Drug-Drug Similarity Networks Based on Drug-Gene Interactions

Drug repurposing is a valuable alternative to traditional drug design based on the assumption that medicines have multiple functions. Computer-based techniques use ever-growing drug databases to uncover new drug repurposing hints, which require further validation with in vitro and in vivo experiments. Indeed, such a scientific undertaking can be particularly effective in the case of rare diseases (resources for developing new drugs are scarce) and new diseases such as COVID-19 (designing new drugs require too much time). This paper introduces a new, completely automated computational drug repurposing pipeline based on drug-gene interaction data. We obtained drug-gene interaction data from an earlier version of DrugBank, built a drug-gene interaction network, and projected it as a drug-drug similarity network (DDSN). We then clustered DDSN by optimizing modularity resolution, used the ATC codes distribution within each cluster to identify potential drug repurposing candidates, and verified repurposing hints with the latest DrugBank ATC codes. Finally, using the best modularity resolution found with our method, we applied our pipeline to the latest DrugBank drug-gene interaction data to generate a comprehensive drug repurposing hint list.

Uncovering New Drug Properties in Target-Based Drug-Drug Similarity Networks

Despite recent advances in bioinformatics, systems biology, and machine learning, the accurate prediction of drug properties remains an open problem. Indeed, because the biological environment is a complex system, the traditional approach—based on knowledge about the chemical structures—can not fully explain the nature of interactions between drugs and biological targets. Consequently, in this paper, we propose an unsupervised machine learning approach that uses the information we know about drug–target interactions to infer drug properties. To this end, we define drug similarity based on drug–target interactions and build a weighted Drug–Drug Similarity Network according to the drug–drug similarity relationships. Using an energy-model network layout, we generate drug communities associated with specific, dominant drug properties. DrugBank confirms the properties of 59.52% of the drugs in these communities, and 26.98% are existing drug repositioning hints we reconstruct with our DDSN approach. The remaining 13.49% of the drugs seem not to match the dominant pharmacologic property; thus, we consider them potential drug repurposing hints. The resources required to test all these repurposing hints are considerable. Therefore we introduce a mechanism of prioritization based on the betweenness/degree node centrality. Using betweenness/degree as an indicator of drug repurposing potential, we select Azelaic acid and Meprobamate as a possible antineoplastic and antifungal, respectively. Finally, we use a test procedure based on molecular docking to analyze Azelaic acid and Meprobamate’s repurposing.

Accelerated Forced Degradation of Therapeutic Peptides in Levitated Microdroplets

PURPOSE

Forced degradation is critical to probe the stabilities and chemical reactivities of therapeutic peptides. Typically performed in bulk followed by LC-UV or LC-MS analysis, this traditional workflow consists of a reaction/analysis sequence and usually requires half a day to several days to form and measure the desired amounts of degradants. A faster method is needed to study peptide degradation in a shorter time in order to speed up the drug development process.

METHODS

In the new rapid method developed in this study, peptide degradation occurs in levitated aqueous microdroplets using the Leidenfrost effect.

RESULTS

This two-minute reaction/analysis workflow allows major degradation pathways of Buserelin, Octreotide, Desmopressin and Leuprorelin to be studied. The reactions include deamidation, disulfide bond cleavage, ether cleavage, peptide bond hydrolysis, and oxidation.

CONCLUSIONS

The accelerated forced degradation method requires a minimal amount of therapeutic peptide per stress condition, and the appropriate extent of degradation can be readily generated in seconds by adjusting the droplet levitation time. Levitated microdroplets should be applicable in pharmaceutical development to rapidly determine the intrinsic stability of therapeutic peptides and to aid formulation development by screening the effects of excipients on the stability of the peptides. Graphical abstract.

Pharmaceutical Cocrystal Drug Products: An Outlook on Product Development

Active pharmaceutical ingredients (APIs) are most commonly formulated and delivered to patients in the solid state. Recently, an alternative API solid-state form, namely the pharmaceutical cocrystal, has witnessed increasing academic and industrial interest due to its potential to deliver bespoke physical properties in the pharmaceutical drug product. This interest has been supported by advances in cocrystal discovery, development, and approval, enabled primarily by a supportive new FDA guidance in February 2018. In this review, we describe the process of developing a pharmaceutical cocrystal drug product from screening to approval, with an emphasis on significant developments over the past decade.

Clustering drug-drug interaction networks with energy model layouts: community analysis and drug repurposing

Analyzing drug-drug interactions may unravel previously unknown drug action patterns, leading to the development of new drug discovery tools. We present a new approach to analyzing drug-drug interaction networks, based on clustering and topological community detection techniques that are specific to complex network science. Our methodology uncovers functional drug categories along with the intricate relationships between them. Using modularity-based and energy-model layout community detection algorithms, we link the network clusters to 9 relevant pharmacological properties. Out of the 1141 drugs from the DrugBank 4.1 database, our extensive literature survey and cross-checking with other databases such as Drugs.com, RxList, and DrugBank 4.3 confirm the predicted properties for 85% of the drugs. As such, we argue that network analysis offers a high-level grasp on a wide area of pharmacological aspects, indicating possible unaccounted interactions and missing pharmacological properties that can lead to drug repositioning for the 15% drugs which seem to be inconsistent with the predicted property. Also, by using network centralities, we can rank drugs according to their interaction potential for both simple and complex multi-pathology therapies. Moreover, our clustering approach can be extended for applications such as analyzing drug-target interactions or phenotyping patients in personalized medicine applications.

Upper critical solution temperature behavior of cinnamic acid and polyethyleneimine mixture and its effect on temperature-dependent release of liposome

The mixture of polyethyleneimine (PEI) and cinnamic acid (CA) in HEPES buffer (pH 7.0) exhibited an upper critical solution temperature in the temperature range of 20-50 °C. CA would be electrostatically conjugated with PEI and the PEI-CA conjugate is thought to act as a thermo-sensitive polymer. On the optical microscope image of PEI/CA mixture, microparticles were found at 25 °C, disappeared when heated to 50 °C, and formed again upon cooling to 25 °C. PEI-CA conjugate was immobilized on the surface of egg phosphatidylcholine (EPC) liposome by adding PEI to the suspension of liposome incorporating CA. The size and the zeta potential of the liposome markedly increased by cooling the liposomal suspension from 50 °C to 20 °C. This could be ascribed to the cooling-induced self-assembling property of PEI-CA conjugate. The release profile of Rhodamine B base from liposome incorporating CA with PEI was investigated while the liposome suspension of 50 °C was exposed to the release medium of 20 °C, 30 °C, 40 °C and 50 °C. The release degree was higher at a lower temperature. When exposed to a lower temperature (20 °C, 30 °C, 40 °C), PEI-CA could be self-assembled and change its configuration on the surface of liposome, promoting the release from the liposome.

Virtual hydrate screening and coformer selection for improved relative humidity stability

The descriptors were determined, which can be most efficiently applied to virtual screening in order to provide answers to the following questions: 1) what is the propensity to form a solid state hydrate of a pharmaceutical compound, and 2) which coformer would provide for the highest stability with respect to relative humidity conditions?

Molecular perspectives on solid-state phase transformation and chemical reactivity of drugs: metoclopramide as an example

Here, I provide an overview of the solid-state characteristics, phase transformations and chemical reactions of metoclopramide hydrochloride monohydrate (MCP HCl H2O). Three unique techniques, including thermoanalytical methods, one-step simultaneous differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) microspectroscopy, and hot-stage microscopic (HSM) imaging, have been applied to study the solid-state phase transitions of MCP HCl H2O in continuous dehydration, amorphization and recrystallization processes. I also review the effects of grinding or heating on ion-exchange reactions, milling, compression or colyophilization on Maillard reactions, and γ-ray irradiation or electron beams on radiolysis in the solid state. I also report the exposure of MCP HCl H2O in solution to light, irradiation, oxidants or π-acceptors. This review will serve as a useful keynote for the evolving realm of solid-state chemistry research.

Synthesis, biological activity, and biopharmaceutical characterization of tacrine dimers as acetylcholinesterase inhibitors

Tacrine (THA), as the first approved acetylcholinesterase (AChE) inhibitors for the treatment of Alzheimer's disease (AD), has been extensively investigated in last seven decades. After dimerization of THA via a 7-carbon alkyl spacer, bis(7)-tacrine (B7T) showed much potent anti-AChE activity than THA. We here report synthesis, biological evaluation and biopharmaceutical characterization of six THA dimers referable to B7T. According to IC50 values, the in vitro anti-AChE activities of THA dimers were up to 300-fold more potent and 200-fold more selective than that of THA. In addition, the anti-AChE activities of THA dimers were found to be associated with the type and length of the linkage. All studied THA dimers showed much lower cytotoxicity than B7T, but like B7T, they demonstrated much lower absorptive permeabilities than that of THA on Caco-2 monolayer model. In addition, all THA dimers demonstrated significant efflux transport (efflux ratio >4), indicating that the limited permeability could be associated with the efflux transport during absorption process. Moreover, the dimer with higher Log P value was accompanied with higher permeability but lower aqueous solubility. A balanced consideration of activity, solubility, cytotoxicity and permeability should be conducted in selection of the potential candidates for further in vivo investigation.

Compound selection for development - is salt formation the ultimate answer? Experiences with an extended concept of the "100mg approach"

In order to select the best candidates for development, physicochemical criteria such as solubility, chemical and physical stability, hygroscopicity, and thermal characteristics need to be evaluated as early as possible and balanced against other important criteria such as pharmacology or pharmacokinetics. It could be shown, that our miniaturized pharmaceutical profiling concept ("100mg approach"), is capable to reliably identify potential development issues of drug candidates, which, therefore, can be approached early on. Salt formation is a well established strategy to improve unfavorable properties, in particular poor solubility. This article describes our stepwise approach on salt screening, including selection criteria, and summarizes the observations we had during compound investigation. Considering a data base of 337 compounds (salts and uncharged substances), experiences with various counterions evaluated over the last 10years are discussed. We realized that salt formation usually improves poor solubility of a given candidate, but this is often at the cost of other attributes being relevant for pharmaceutical development. Surprisingly, in more than 50% of all cases the "free form" was finally selected after carefully weighing all compound characteristics. Therefore, we conclude that an early salt selection strategy is of utmost importance to predict potential development issues and to enable the provision of alternative physical forms. However, salt formation itself is not necessarily the best solution to meet all development requirements. The selection of a free form (acid or base) in combination with advanced formulation strategies should always be considered, sometimes as best compromise.

Strategies to address low drug solubility in discovery and development

Drugs with low water solubility are predisposed to low and variable oral bioavailability and, therefore, to variability in clinical response. Despite significant efforts to "design in" acceptable developability properties (including aqueous solubility) during lead optimization, approximately 40% of currently marketed compounds and most current drug development candidates remain poorly water-soluble. The fact that so many drug candidates of this type are advanced into development and clinical assessment is testament to an increasingly sophisticated understanding of the approaches that can be taken to promote apparent solubility in the gastrointestinal tract and to support drug exposure after oral administration. Here we provide a detailed commentary on the major challenges to the progression of a poorly water-soluble lead or development candidate and review the approaches and strategies that can be taken to facilitate compound progression. In particular, we address the fundamental principles that underpin the use of strategies, including pH adjustment and salt-form selection, polymorphs, cocrystals, cosolvents, surfactants, cyclodextrins, particle size reduction, amorphous solid dispersions, and lipid-based formulations. In each case, the theoretical basis for utility is described along with a detailed review of recent advances in the field. The article provides an integrated and contemporary discussion of current approaches to solubility and dissolution enhancement but has been deliberately structured as a series of stand-alone sections to allow also directed access to a specific technology (e.g., solid dispersions, lipid-based formulations, or salt forms) where required.

Impact of preformulation on drug development

INTRODUCTION

Preformulation assists scientists in screening lead candidates based on their physicochemical and biopharmaceutical properties. This data is useful for selection of new chemical entities (NCEs) for preclinical efficacy/toxicity studies which is a major section under investigational new drug application. A strong collaboration between discovery and formulation group is essential for selecting right NCEs in order to reduce attrition rate in the late stage development.

AREAS COVERED

This article describes the significance of preformulation research in drug discovery and development. Various crucial preformulation parameters with case studies have been discussed.

EXPERT OPINION

Physicochemical and biopharmaceutical characterization of NCEs is a decisive parameter during product development. Early prediction of these properties helps in selecting suitable physical form (salt, polymorph, etc.) of the candidate. Based on pharmacokinetic and efficacy/toxicity studies, suitable formulation for Phase I clinical studies can be developed. Overall these activities contribute in streamlining efficacy/toxicology evaluation, allowing pharmacologically effective and developable molecules to reach the clinic and eventually to the market. In this review, the magnitude of understanding preformulation properties of NCEs and their utility in product development has been elaborated with case studies.

Advances in simultaneous DSC-FTIR microspectroscopy for rapid solid-state chemical stability studies: some dipeptide drugs as examples

The solid-state chemistry of drugs has seen growing importance in the pharmaceutical industry for the development of useful API (active pharmaceutical ingredients) of drugs and stable dosage forms. The stability of drugs in various solid dosage forms is an important issue because solid dosage forms are the most common pharmaceutical formulation in clinical use. In solid-state stability studies of drugs, an ideal accelerated method must not only be selected by different complicated methods, but must also detect the formation of degraded product. In this review article, an analytical technique combining differential scanning calorimetry and Fourier-transform infrared (DSC-FTIR) microspectroscopy simulates the accelerated stability test, and simultaneously detects the decomposed products in real time. The pharmaceutical dipeptides aspartame hemihydrate, lisinopril dihydrate, and enalapril maleate either with or without Eudragit E were used as testing examples. This one-step simultaneous DSC-FTIR technique for real-time detection of diketopiperazine (DKP) directly evidenced the dehydration process and DKP formation as an impurity common in pharmaceutical dipeptides. DKP formation in various dipeptides determined by different analytical methods had been collected and compiled. Although many analytical methods have been applied, the combined DSC-FTIR technique is an easy and fast analytical method which not only can simulate the accelerated drug stability testing but also at the same time enable to explore phase transformation as well as degradation due to thermal-related reactions. This technique offers quick and proper interpretations.

Preformulation studies of Zidovudine derivatives: Acid dissociation constants, differential scanning calorimetry, thermogravimetry, x-ray powder diffractometry and aqueous stability studies

As part as of the preformulation studies of new 5'-OH derivatives of zidovudine, compounds 2-6, their acid dissociation constants, Differential Scanning Calorimetry (DSC) and Thermogravimetry (TG) curves, X-Ray Powder diffractograms and aqueous stability are reported. A sensitive technique such as differential scanning potentiometry was used to determine the pKa constants of the above mentioned compounds. In addition, pKa values were calculated from theoretical methods, and no significant differences with those of experimental ones were observed. X-Ray Powder Diffractometry data demonstrated that compounds 2-4 were crystalline while 5 and 6 were amorphous. DSC analysis indicated that all of them presented an exothermic decomposition peak above 150 °C which is accompanied by a weight loss in the respective TG curves. The stability of these compounds in aqueous medium at different pH values was investigated, using a validated High Performance Liquid Chromatography (HPLC) method, which demonstrated to be rapid, selective, sensitive, accurate and stability-indicating. Good recovery, linearity and precision were also achieved. For all compounds the aqueous hydrolysis followed a pseudo-first-order kinetics, depending on pH and the union existing between AZT and the associate moiety. The hydrolysis was catalyzed by hydroxide ion in the 7.4-13.2 pH range, while all compounds exhibited pH-independent stability from acidic to neutral media (pHs 1.0-7.4).

Early development drug formulation on a chip: fabrication of nanoparticles using a microfluidic spray dryer

Early development drug formulation is exacerbated by increasingly poor bioavailability of potential candidates. Prevention of attrition due to formulation problems necessitates physicochemical analysis and formulation studies at a very early stage during development, where the availability of a new substance is limited to small quantities, thus impeding extensive experiments. Miniaturization of common formulation processes is a strategy to overcome those limitations. We present a versatile technique for fabricating drug nanoformulations using a microfluidic spray dryer. Nanoparticles are formed by evaporative precipitation of the drug-loaded spray in air at room temperature. Using danazol as a model drug, amorphous nanoparticles of 20-60 nm in diameter are prepared with a narrow size distribution. We design the device with a geometry that allows the injection of two separate solvent streams, thus enabling co-spray drying of two substances for the production of drug co-precipitates with tailor-made composition for optimization of therapeutic efficiency.

Evaluation of physical and chemical changes in pharmaceuticals flown on space missions

Efficacy and safety of medications used for the treatment of astronauts in space may be compromised by altered stability in space. We compared physical and chemical changes with time in 35 formulations contained in identical pharmaceutical kits stowed on the International Space Station (ISS) and on Earth. Active pharmaceutical content (API) was determined by ultra- and high-performance liquid chromatography after returning to Earth. After stowage for 28 months in space, six medications aboard the ISS and two of matching ground controls exhibited changes in physical variables; nine medications from the ISS and 17 from the ground met the United States Pharmacopeia (USP) acceptance criteria for API content after 28 months of storage. A higher percentage of medications from each flight kit had lower API content than the respective ground controls. The number of medications failing API requirement increased as a function of time in space, independent of expiration date. The rate of degradation was faster in space than on the ground for many of the medications, and most solid dosage forms met USP standard for dissolution after storage in space. Cumulative radiation dose was higher and increased with time in space, whereas temperature and humidity remained similar to those on the ground. Exposure to the chronic low dose of ionizing radiation aboard the spacecraft as well as repackaging of solid dosage forms in flight-specific dispensers may adversely affect stability of pharmaceuticals. Characterization of degradation profiles of unstable formulations and identification of chemical attributes of stability in space analog environments on Earth will facilitate development of space-hardy medications.