An historical overview of drug discovery

The Millennia-Long Development of Drugs Associated with the 80-Year-Old Artificial Intelligence Story: The Therapeutic Big Bang?

The journey of drug discovery (DD) has evolved from ancient practices to modern technology-driven approaches, with Artificial Intelligence (AI) emerging as a pivotal force in streamlining and accelerating the process. Despite the vital importance of DD, it faces challenges such as high costs and lengthy timelines. This review examines the historical progression and current market of DD alongside the development and integration of AI technologies. We analyse the challenges encountered in applying AI to DD, focusing on drug design and protein-protein interactions. The discussion is enriched by presenting models that put forward the application of AI in DD. Three case studies are highlighted to demonstrate the successful application of AI in DD, including the discovery of a novel class of antibiotics and a small-molecule inhibitor that has progressed to phase II clinical trials. These cases underscore the potential of AI to identify new drug candidates and optimise the development process. The convergence of DD and AI embodies a transformative shift in the field, offering a path to overcome traditional obstacles. By leveraging AI, the future of DD promises enhanced efficiency and novel breakthroughs, heralding a new era of medical innovation even though there is still a long way to go.

Phenotypic drug discovery: a case for thymosin alpha-1

Phenotypic drug discovery (PDD) involves screening compounds for their effects on cells, tissues, or whole organisms without necessarily understanding the underlying molecular targets. PDD differs from target-based strategies as it does not require knowledge of a specific drug target or its role in the disease. This approach can lead to the discovery of drugs with unexpected therapeutic effects or applications and allows for the identification of drugs based on their functional effects, rather than through a predefined target-based approach. Ultimately, disease definitions are mostly symptom-based rather than mechanism-based, and the therapeutics should be likewise. In recent years, there has been a renewed interest in PDD due to its potential to address the complexity of human diseases, including the holistic picture of multiple metabolites engaging with multiple targets constituting the central hub of the metabolic host-microbe interactions. Although PDD presents challenges such as hit validation and target deconvolution, significant achievements have been reached in the era of big data. This article explores the experiences of researchers testing the effect of a thymic peptide hormone, thymosin alpha-1, in preclinical and clinical settings and discuss how its therapeutic utility in the precision medicine era can be accommodated within the PDD framework.

Parallel Synthesis of Piperazine Tethered Thiazole Compounds with Antiplasmodial Activity

Thiazole and piperazine are two important heterocyclic rings that play a prominent role in nature and have a broad range of applications in agricultural and medicinal chemistry. Herein, we report the parallel synthesis of a library of diverse piperazine-tethered thiazole compounds. The reaction of piperazine with newly generated 4-chloromethyl-2-amino thiazoles led to the desired piperazine thiazole compounds with high purities and good overall yields. Using a variety of commercially available carboxylic acids, the parallel synthesis of a variety of disubstituted 4-(piperazin-1-ylmethyl)thiazol-2-amine derivatives is described. the screening of the compounds led to the identification of antiplasmodial compounds that exhibited interesting antimalarial activity, primarily against the Plasmodium falciparum chloroquine-resistant Dd2 strain. The hit compound 2291-61 demonstrated an antiplasmodial EC50 of 102 nM in the chloroquine-resistant Dd2 strain and a selectivity of over 140.

Gender representation in drug development studies for diabetes mellitus. A systematic review

BACKGROUND

During the last 20 years, the prevalence of diabetes mellitus (DM) has increased drastically, and so has the number of associated medicine and drug development studies. Despite knowing that men and women respond differently to DM medicines, biological gender differences still tend not to be prioritized during medicine development.

OBJECTIVE

This study examined gender representation in medicine development studies for DM.

METHOD

We conducted a systematic review, and in February 2022, we searched EMBASE (Excerpta Medica Database), MEDLINE (Medical Literature Analysis and Retrieval System Online) and PubMed using a block search strategy. Randomized controlled studies (RCTs) including people diagnosed with DM (any type) aged 18-65 years were included. The Consolidated Standards of Reporting Trial 2010 checklist was applied to assess the studies' reported quality. The results are presented in a narrative synthesis.

RESULTS

Nine studies met the inclusion criteria. On average, women represented 31.4% of study participants, and similarly, for each trial phase, women were less represented than men.

CONCLUSION

This review showed an unequal gender representation in drug development studies for DM, with women and men representing 31.4% and 68.6% of the study participants, respectively, in the included studies. However, gender differences in medical drug studies might be due to specific exclusion criteria, participants' behaviour toward attending in medicine development or the law in the country of origin.

Peptidomics

Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.

Applications and prospects of cryo-EM in drug discovery

Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time- and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy (cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence (AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of medium-resolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.

Framing access to essential medicines in the context of Universal Health Coverage: a critical analysis of health sector strategic plans from eight countries in the WHO African region

BACKGROUND

Framing affects how issues are understood and portrayed. This profoundly shapes the construction of social problems and how policy options are considered. While access to essential medicines (ATM) in the World Health Organization (WHO) African Region is often framed as a societal problem, there is dominance of medical and technically oriented approaches to analyze and remedy the situation. Hence, the systematic application of social science approaches, such as framing theory, remains under-explored. Through a framing analysis of National Strategic Plans (NSPs) from eight countries, this study explores the applicability and potential usefulness of framing theory to analyze essential medicines policies.

METHODS

We inductively coded the relevant NSP textual fragments using the qualitative content analysis software ATLAS.ti.22. Benford and Snow's conceptualization of framing was used to organize the coded data into three frames: diagnostic (problems), prognostic (solutions) and motivational (values and ideological).

RESULTS

The following five diagnostic frames were dominant or in-frame: medicine unavailability, ineffective regulation, weak supply chain management, proliferation of counterfeit (substandard or falsified) medicines and use of poor quality medicines. Diagnostic frames related to financing, affordability, efficiency and corruption were given limited coverage or out of frame. Prognostic frames corresponded with how these problems were framed. Whilst Universal Health Coverage (UHC) and its guiding principles was the dominant motivational frame, we identified some frame discordance between the global discourse and national level policies.

CONCLUSIONS

Social science approaches such as framing analysis are applicable and useful to systematically analyze essential medicine aspects. By applying framing theory, we revealed that ATM aspects in the eight countries we analyzed are more often characterized in relation to availability at the expense of affordability which undermines UHC. We conclude that whilst UHC is a strong motivational frame to guide ATM aspects, it is insufficient to inform a comprehensive approach to address the problems related to ATM at country level. To effectively advance ATM, concerned actors need to realize such limitation and endeavor to gain a deeper understanding of how problems are framed and agendas are set at country level, the processes through which ideas and knowledge become policies, including the political demands, incentives and trade-offs facing decision-makers in selecting policy priorities.

Human Genomics and Drug Development

Insights into the genetic basis of human disease are helping to address some of the key challenges in new drug development including the very high rates of failure. Here we review the recent history of an emerging, genomics-assisted approach to pharmaceutical research and development, and its relationship to Mendelian randomization (MR), a well-established analytical approach to causal inference. We demonstrate how human genomic data linked to pharmaceutically relevant phenotypes can be used for (1) drug target identification (mapping relevant drug targets to diseases), (2) drug target validation (inferring the likely effects of drug target perturbation), (3) evaluation of the effectiveness and specificity of compound-target engagement (inferring the extent to which the effects of a compound are exclusive to the target and distinguishing between on-target and off-target compound effects), and (4) the selection of end points in clinical trials (the diseases or conditions to be evaluated as trial outcomes). We show how genomics can help identify indication expansion opportunities for licensed drugs and repurposing of compounds developed to clinical phase that proved safe but ineffective for the original intended indication. We outline statistical and biological considerations in using MR for drug target validation (drug target MR) and discuss the obstacles and challenges for scaled applications of these genomics-based approaches.

From Lock-In to Transformation: A Path-Centric Theory of Emerging Technology and Organizing

We offer a path-centric theory of emerging technology and organizing that addresses a basic question. When does emerging technology lead to transformative change? A path-centric perspective on technology focuses on the patterns of actions afforded by technology in use. We identify performing and patterning as self-reinforcing mechanisms that shape patterns of action in the domain of emerging technology and organizing. We use a dynamic simulation to show that performing and patterning can lead to a wide range of trajectories, from lock-in to transformation, depending on how emerging technology in use influences the pattern of action. When emerging technologies afford new actions that can be flexibly recombined to generate new paths, decisive transformative effects are more likely. By themselves, new affordances are not likely to generate transformation. We illustrate this theory with examples from the practice of pharmaceutical drug discovery. The path-centric perspective offers a new way to think about generativity and the role of affordances in organizing.

Synergistic bactericidal profiling of prodigiosin extracted from Serratia marcescens in combination with antibiotics against pathogenic bacteria

The emergence of multidrug-resistant (MDR) bacteria is on the rise and the situation has been worsening with each passing day, which is evident from the outpouring number of reports about how more and more pathogens are becoming resistant to even the third and fourth generations of antibiotics. Lately, combination therapies or drug synergy have been giving promising results in curbing infections since it delineates its action on multiple aspects as compared to monotherapies. In this study, we used prodigiosin, a bacterial pigment endowed with magnificent biological properties, in combination with six antibiotics to study its effect on Pseudomonas aeruginosa, Staphylococcus aureus and Chromobacterium violaceum. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of prodigiosin against the test organisms was determined and a checkerboard assay of prodigiosin with various antibiotic combinations was performed with an aim to abate antimicrobial resistance. MIC and MBC of prodigiosin was obtained in the range of 4–16 μg/mL, which was lower than that of most test antibiotics. Coupling prodigiosin with other test antibiotics exhibited an excellent synergy profile against all test organisms and the effects were reported to be either synergistic or additive. In the case of S. aureus and C. violaceum, all combinations were found to be synergic, and remarkably for S. aureus, FBC index was reported to be as low as ≤0.25 with all of the test antibiotics. Therefore, it is deduced that prodigiosin augments and intensifies the action of antibiotics, and results in a double-whammy against the MDR strains.

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Prodigiosin showed excellent bactericidal activity against P. aeruginosa, S. aureus and C. violaceum.

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Prodigiosin in combination with antibiotics exhibited synergic effect in majority of the cases against all test pathogens.

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For S. aureus, prodigiosin-antibiotic combinations showed excellent synergic effect with an FBC index as low as ≤0.25.

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Prodigiosin augments the action of antibiotics against pathogenic bacteria.

The Convergence of Stem Cell Technologies and Phenotypic Drug Discovery

Recent advances in induced pluripotent stem cell technologies and phenotypic screening shape the future of bioactive small-molecule discovery. In this review we analyze the impact of small-molecule phenotypic screens on drug discovery as well as on the investigation of human development and disease biology. We further examine the role of 3D spheroid/organoid structures, microfluidic systems, and miniaturized on-a-chip systems for future discovery strategies. In highlighting representative examples, we analyze how recent achievements can translate into future therapies. Finally, we discuss remaining challenges that need to be overcome for the adaptation of the next generation of screening approaches.

Target-based whole-cell screening by ¹H NMR spectroscopy

An NMR-based approach marries the two traditional screening technologies (phenotypic and target-based screening) to find compounds inhibiting a specific enzymatic reaction in bacterial cells. Building on a previous study in which it was demonstrated that hydrolytic decomposition of meropenem in living Escherichia coli cells carrying New Delhi metallo-β-lactamase subclass 1 (NDM-1) can be monitored in real time by NMR spectroscopy, we designed a cell-based NMR screening platform. A strong NDM-1 inhibitor was identified with cellular IC50 of 0.51 μM, which is over 300-fold more potent than captopril, a known NDM-1 inhibitor. This new screening approach has great potential to be applied to targets in other cell types, such as mammalian cells, and to targets that are only stable or functionally competent in the cellular environment.

The chemistry and biology of soluble guanylate cyclase stimulators and activators

The vasodilatory properties of nitric oxide (NO) have been utilized in pharmacotherapy for more than 130 years. Still today, NO-donor drugs are important in the management of cardiovascular diseases. However, inhaled NO or drugs releasing NO and organic nitrates are associated with noteworthy therapeutic shortcomings, including resistance to NO in some disease states, the development of tolerance during long-term treatment, and nonspecific effects, such as post-translational modification of proteins. The beneficial actions of NO are mediated by stimulation of soluble guanylate cyclase (sGC), a heme-containing enzyme which produces the intracellular signaling molecule cyclic guanosine monophosphate (cGMP). Recently, two classes of compounds have been discovered that amplify the function of sGC in a NO-independent manner, the so-called sGC stimulators and sGC activators. The most advanced drug, the sGC stimulator riociguat, has successfully undergone Phase III clinical trials for different forms of pulmonary hypertension.

Phenotypic screens as a renewed approach for drug discovery

The significant reduction in the number of newly approved drugs in the past decade has been partially attributed to failures in discovery and validation of new targets. Evaluation of recently approved new drugs has revealed that the number of approved drugs discovered through phenotypic screens, an original drug screening paradigm, has exceeded those discovered through the molecular target-based approach. Phenotypic screening is thus gaining new momentum in drug discovery with the hope that this approach may revitalize drug discovery and improve the success rate of drug approval through the discovery of viable lead compounds and identification of novel drug targets.

Use of allosteric targets in the discovery of safer drugs

The need for drugs with fewer side effects cannot be overemphasized. Today, most drugs modify the actions of enzymes, receptors, transporters and other molecules by directly binding to their active (orthosteric) sites. However, orthosteric site configuration is similar in several proteins performing related functions and this leads to a lower specificity of a drug for the desired protein. Consequently, such drugs may have adverse side effects. A new basis of drug discovery is emerging based on the binding of the drug molecules to sites away (allosteric) from the orthosteric sites. It is possible to find allosteric sites which are unique and hence more specific as targets for drug discovery. Of many available examples, two are highlighted here. The first is caloxins - a new class of highly specific inhibitors of plasma membrane Ca²⁺ pumps. The second concerns the modulation of receptors for the neurotransmitter acetylcholine, which binds to 12 types of receptors. Exploitation of allosteric sites has led to the discovery of drugs which can selectively modulate the activation of only 1 (M1 muscarinic) out of the 12 different types of acetylcholine receptors. These drugs are being tested for schizophrenia treatment. It is anticipated that the drug discovery exploiting allosteric sites will lead to more effective therapeutic agents with fewer side effects.

Synthesis, characterization of penicillin G capped silver nanoconjugates to combat β-lactamase resistance in infectious microorganism

In the present study, a novel strategy was adopted to synthesize, β lactamase resistant penicillin G molecules by using the unique properties of silver nanoparticles. Ascorbic acid-stabilized spherical monodispersed silver nanoparticles were prepared by a simple chemical reaction. The formation processes of the silver nanoparticles were investigated by UV-vis spectroscopy and Atomic Force Microscopy (AFM). Free amine groups were introduced on the surface of native silver nanoparticles by coating a uniform layer of polyaniline and this was confirmed by FTIR spectroscopy and Scanning Electron Microscopy. Functionalized silver nanoparticles were then grafted to the C3 carboxyl group of the β lactam ring of penicillin G in the presence of N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDAC) with a conjugation yield of 213 μg mg⁻¹. These novel silver penicillin G nanoconjugates showed a very good growth inhibition against both non-resistant Escherichia coli (gram negative) as well as toward β lactam resistant, E. coli (gram negative) and Staphylococcus aureus (gram positive).