Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles

Unravelling the mode of action of the Tres Cantos Antimalarial Set (TCAMS): investigating the mechanism of potent antimalarial compounds potentially targeting the human serotonin receptor

BACKGROUND

Despite the strides made in recent decades, the resistance observed in existing antimalarial drugs, and the intricate life cycle of the Plasmodium parasite underscore the pressing need to develop novel and effective therapeutic interventions. This article provides a comprehensive evaluation of the outcomes stemming from screening a library comprising 48 compounds (TCAMS) against Plasmodium falciparum.

METHODS

This study focused on characterizing the IC50 values of compounds from the Tres Cantos Antimalarial Set (TCAMS) library via a double-labelling method of P. falciparum parasites with SYBR Green-I and MitoTracker Deep Red, which were evaluated via flow cytometry. Evaluation of the cytotoxicity of the best candidates in human embryonic kidney (HEK293) cells, chemoinformatic analysis, and exploration of the effects of the compounds on the action of serotonin and melatonin in the erythrocytic life cycle of the parasite.

RESULTS

IC50 characterization confirmed that 93.75% of the compounds tested exhibited antimalarial activity at concentrations below 2 micromolar (µM), with 5 compounds showing IC50 values below 50 nM (nM) (15.21 ± 5.97 nM to 45.82 ± 5.11 nM). Furthermore, 12 compounds presented IC50 values between 50 and 100 nM (57.43 ± 12.25 nM to 100.6 ± 22.89 nM), highlighting their potent in vitro efficacy against P. falciparum. Cytotoxicity evaluation in HEK293 cells revealed that 12 from 17 compounds did not significantly reduce cell viability. Cheminformatics analysis clustered the compounds based on structural and physicochemical similarities, revealing distinct structural patterns. Exploration of hypothetical targets from the TCAMS library identified 27 compounds with potential targets, 15 specifically targeted serotonergic receptors. Subsequent serotonin and melatonin treatment experiments indicated that certain compounds could inhibit both effects on parasitaemia, suggesting a complex interaction with signaling in P. falciparum.

CONCLUSIONS

This study identifies promising antimalarial candidates with low IC50 values and highlights the significance of targeting serotonin receptors in the development of potential antimalarial drugs.

Another decade of antimalarial drug discovery: New targets, tools and molecules

Malaria remains a devastating but preventable infectious disease that disproportionately affects the African continent. Emerging resistance to current frontline therapies means that not only are new treatments urgently required, but also novel validated antimalarial targets to circumvent cross-resistance. Fortunately, tremendous efforts have been made by the global drug discovery community over the past decade. In this chapter, we will highlight some of the antimalarial drug discovery and development programmes currently underway across the globe, charting progress in the identification of new targets and the development of new classes of drugs to prosecute them. These efforts have been complemented by the development of valuable tools to accelerate target validation such as the NOD scid gamma (NSG) humanized mouse efficacy model and progress in predictive modelling and open-source software. Among the medicinal chemistry programmes that have been conducted over the past decade are those targeting Plasmodium falciparum ATPase4 (ATP4) and acetyl-CoA synthetase (AcAS) as well as proteins disrupting parasite protein translation such as the aminoacyl-tRNA synthetases (aaRSs) and eukaryotic elongation factor 2 (eEF2). The benefits and challenges of targeting Plasmodium kinases will be examined, with a focus on Plasmodium cyclic GMP-dependent protein kinase (PKG), cyclin-dependent-like protein kinase 3 (CLK3) and phosphatidylinositol 4-kinase (PI4K). The chapter concludes with a survey of incipient drug discovery centres in Africa and acknowledges the value of recent international meetings in galvanizing and uniting the antimalarial drug discovery community.

Open Source Code Contributions to Global Health: The Case of Antimalarial Drug Discovery

The discovery of treatments for infectious diseases that affect the poorest countries has been stagnant for decades. As long as expected returns on investment remain low, pharmaceutical companies' lack of interest in this disease area must be compensated for with collaborative efforts from the public sector. New approaches to drug discovery, inspired by the "open source" philosophy prevalent in software development, offer a platform for experts from diverse backgrounds to contribute their skills, enhancing reproducibility, progress tracking, and public discussion. Here, we present the first efforts of Ersilia, an initiative focused on attracting data scientists into contributing to global health, toward meeting the goals of Open Source Malaria, a consortium of medicinal chemists investigating antimalarial compounds using a purely open science approach. We showcase the chemical space exploration of a set of triazolopyrazine compounds with potent antiplasmodial activity and discuss how open source practices can serve as a common ground to make drug discovery more inclusive and participative.

Metal-Free Nitrogen-Doped Mesoporous Carbons for the Mild and Selective Synthesis of Pyrroles from Nitroarenes via Cascade Reaction

The cascade synthesis of pyrroles from nitroarenes is an attractive alternative strategy. However, metal catalysts and relatively high temperatures cover the existing reported catalytic systems for this strategy. The development of nonmetallic heterogeneous catalytic systems for the one-pot synthesis of pyrrole from nitroarenes under mild conditions is both worthwhile and challenging. Herein, we describe an exceptionally efficient method for the synthesis of N-substituted pyrroles by the reductive coupling of nitroarenes and diketones over heterogeneous metal-free catalysts under mild conditions. Nonmetallic NC-X catalysts with high activity were prepared from the pyrolysis of well-defined ligands via simple sacrificing hard template methods. Hydrazine hydrate, formic acid, and molecular hydrogen can all be used as reducing agents in the hydrogenation/Paal-Knorr reaction sequence to efficiently synthesize various N-substituted pyrroles, including drugs and bioactive molecules. The catalytic system was featured with good tolerance to sensitive functional groups and no side reactions such as dehalogenation and aromatics hydrogenation. Hammett correlation studies have shown that the electron-donating substituents are beneficial for the one-pot synthesis of N-substituted pyrroles. The results established that the outstanding performance of the catalyst is mainly attributed to the contribution of graphitic N in the catalyst as well as the promotion effect of the mesoporous structure on the reaction.

Optimisation-based modelling for explainable lead discovery in malaria

BACKGROUND

The search for new antimalarial treatments is urgent due to growing resistance to existing therapies. The Open Source Malaria (OSM) project offers a promising starting point, having extensively screened various compounds for their effectiveness. Further analysis of the chemical space surrounding these compounds could provide the means for innovative drugs.

METHODS

We report an optimisation-based method for quantitative structure-activity relationship (QSAR) modelling that provides explainable modelling of ligand activity through a mathematical programming formulation. The methodology is based on piecewise regression principles and offers optimal detection of breakpoint features, efficient allocation of samples into distinct sub-groups based on breakpoint feature values, and insightful regression coefficients. Analysis of OSM antimalarial compounds yields interpretable results through rules generated by the model that reflect the contribution of individual fingerprint fragments in ligand activity prediction. Using knowledge of fragment prioritisation and screening of commercially available compound libraries, potential lead compounds for antimalarials are identified and evaluated experimentally via a Plasmodium falciparum asexual growth inhibition assay (PfGIA) and a human cell cytotoxicity assay.

CONCLUSIONS

Three compounds are identified as potential leads for antimalarials using the methodology described above. This work illustrates how explainable predictive models based on mathematical optimisation can pave the way towards more efficient fragment-based lead discovery as applied in malaria.

Open Source Antibiotics: Simple Diarylimidazoles Are Potent against Methicillin-Resistant Staphylococcus aureus

Antimicrobial resistance (AMR) is widely acknowledged as one of the most serious public health threats facing the world, yet the private sector finds it challenging to generate much-needed medicines. As an alternative discovery approach, a small array of diarylimidazoles was screened against the ESKAPE pathogens, and the results were made publicly available through the Open Source Antibiotics (OSA) consortium (https://github.com/opensourceantibiotics). Of the 18 compounds tested (at 32 μg/mL), 15 showed >90% growth inhibition activity against methicillin-resistant Staphylococcus aureus (MRSA) alone. In the subsequent hit-to-lead optimization of this chemotype, 147 new heterocyclic compounds containing the diarylimidazole and other core motifs were synthesized and tested against MRSA, and their structure-activity relationships were identified. While potent, these compounds have moderate to high intrinsic clearance and some associated toxicity. The best overall balance of parameters was found with OSA_975, a compound with good potency, good solubility, and reduced intrinsic clearance in rat hepatocytes. We have progressed toward the knowledge of the molecular target of these phenotypically active compounds, with proteomic techniques suggesting TGFBR1 is potentially involved in the mechanism of action. Further development of these compounds toward antimicrobial medicines is available to anyone under the licensing terms of the project.

Hydrazone-Tethered 5-(Pyridin-4-yl)-4H-1,2,4-triazole-3-thiol Hybrids: Synthesis, Characterisation, in silico ADME Studies, and in vitro Antimycobacterial Evaluation and Cytotoxicity

Compounds containing arylpyrrole-, 1,2,4-triazole- and hydrazone structural frameworks have been widely studied and demonstrated to exhibit a wide range of pharmacological properties. Herein, an exploratory series of new 1,2,4-triazole derivatives designed by amalgamation of arylpyrrole and 1,2,4-triazole structural units via a hydrazone linkage is reported. The synthesised compounds were tested in vitro for their potential activity against Mycobacterium tuberculosis (MTB) H₃₇ Rv strain. The most promising compound 13 - the derivative without the benzene ring appended to the pyrrole unit displayed acceptable activity (MIC₉₀ =3.99 μM) against MTB H₃₇ Rv, while other compounds from the series exhibited modest to weak antimycobacterial activity with MIC₉₀ values in the range between 7.0 and >125 μM. Furthermore, in silico results, predicated using the SwissADME web tool, show that the prepared compounds display desirable ADME profile with parameters within acceptable range.

Discovery of Novel Thiazolidinedione-Derivatives with Multi-Modal Antidiabetic Activities In Vitro and In Silico

Diabetes mellitus (DM) and related complications continue to exert a significant burden on health care systems globally. Although conventional pharmacological therapies are beneficial in the management of this metabolic condition, it is still necessary to seek novel potential molecules for its management. On this basis, we have synthesised and evaluated the anti-diabetic properties of four novel thiazolidinedione (TZD)-derivatives. The TZD derivatives were synthesised through the pharmacophore hybridisation strategy based on N-arylpyrrole and TZD. The resultant derivatives at different concentrations were screened against key enzymes of glucose metabolism and glucose utilisation in the liver (HEP-G2) cell line. Additionally, peroxisome proliferator-activated receptor-γ activation was performed through docking studies. Docking of these molecules against PPAR-γ predicted strong binding, similar to that of rosiglitazone. Hence, TZDD2 was able to increase glucose uptake in the liver cells as compared to the control. The enzymatic inhibition assays showed a relative inhibition activity; with all four derivatives exhibiting ≥ 50% inhibition activity in the α-amylase inhibition assay and a concentration dependent activity in the α-glucosidase inhibition assay. All four derivatives exhibited ≥30% inhibition in the aldose reductase inhibition assay, except TZDD1 at 10 µg/mL. Interestingly, TZDD3 showed a decreasing inhibition activity. In the dipeptidyl peptidase-4 inhibition assay, TZDD2 and TZDD4 exhibited ≥20% inhibition activity.

Discovering New Natural Products Using Metabolomics-Based Approaches

The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.

Tapping into the antitubercular potential of 2,5-dimethylpyrroles: A structure-activity relationship interrogation

An exploration of the chemical space around a 2,5-dimethylpyrrole scaffold of antitubercular hit compound 1 has led to the identification of new derivatives active against Mycobacterium tuberculosis and multidrug-resistant clinical isolates. Analogues incorporating a cyclohexanemethyl group on the methyleneamine side chain at C3 of the pyrrole core, including 5n and 5q, exhibited potent inhibitory effects against the M. tuberculosis strains, substantiating the essentiality of the moiety to their antimycobacterial activity. In addition, selected derivatives showed promising cytotoxicity profiles against human pulmonary fibroblasts and/or murine macrophages, proved to be effective in inhibiting the growth of intracellular mycobacteria, and elicited either bactericidal effects, or bacteriostatic activity comparable to 1. Computational studies revealed that the new compounds bind to the putative target, MmpL3, in a manner similar to that of known inhibitors BM212 and SQ109.

Making the collective knowledge of chemistry open and machine actionable

Large amounts of data are generated in chemistry labs-nearly all instruments record data in a digital form, yet a considerable proportion is also captured non-digitally and reported in ways non-accessible to both humans and their computational agents. Chemical research is still largely centred around paper-based lab notebooks, and the publication of data is often more an afterthought than an integral part of the process. Here we argue that a modular open-science platform for chemistry would be beneficial not only for data-mining studies but also, well beyond that, for the entire chemistry community. Much progress has been made over the past few years in developing technologies such as electronic lab notebooks that aim to address data-management concerns. This will help make chemical data reusable, however it is only one step. We highlight the importance of centring open-science initiatives around open, machine-actionable data and emphasize that most of the required technologies already exist-we only need to connect, polish and embrace them.

Considerations for implementing electronic laboratory notebooks in an academic research environment

As research becomes predominantly digitalized, scientists have the option of using electronic laboratory notebooks to record and access entries. These systems can more readily meet volume, complexity, accessibility and preservation requirements than paper notebooks. Although the technology can yield many benefits, these can be realized only by choosing a system that properly fulfills the requirements of a given context. This review explores the factors that should be considered when introducing electronic laboratory notebooks to an academically focused research group. We cite pertinent studies and discuss our own experience implementing a system within a multidisciplinary research environment. We also consider how the required financial and time investment is shared between individuals and institutions. Finally, we discuss how electronic laboratory notebooks fit into the broader context of research data management. This article is not a product review; it provides a framework for both the initial consideration of an electronic laboratory notebook and the evaluation of specific software packages.

Target 2035 - update on the quest for a probe for every protein

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.

An Open Drug Discovery Competition: Experimental Validation of Predictive Models in a Series of Novel Antimalarials

The Open Source Malaria (OSM) consortium is developing compounds that kill the human malaria parasite, Plasmodium falciparum, by targeting PfATP4, an essential ion pump on the parasite surface. The structure of PfATP4 has not been determined. Here, we describe a public competition created to develop a predictive model for the identification of PfATP4 inhibitors, thereby reducing project costs associated with the synthesis of inactive compounds. Competition participants could see all entries as they were submitted. In the final round, featuring private sector entrants specializing in machine learning methods, the best-performing models were used to predict novel inhibitors, of which several were synthesized and evaluated against the parasite. Half possessed biological activity, with one featuring a motif that the human chemists familiar with this series would have dismissed as "ill-advised". Since all data and participant interactions remain in the public domain, this research project "lives" and may be improved by others.

SO2F2-Mediated N-Alkylation of Imino-Thiazolidinones

The N-alkylation of ambident and weakly nucleophilic imino-thiazolidinones has been developed via substitution with alkyl fluorosulfonates. These reactive electrophiles are obtained through the transformation of nontoxic, economic, and commercially available alcohol derivatives on exposure to SO₂F₂ gas. The use of electron-withdrawing groups and DMAc as solvent affords a (Z)- and N-endocyclic selectivity for the easy introduction of a variety of alkyl and polyfluoroalkyl chains.

There is no market for new antibiotics: this allows an open approach to research and development

There is an increasingly urgent need for new antibiotics, yet there is a significant and persistent economic problem when it comes to developing such medicines. The problem stems from the perceived need for a "market" to drive commercial antibiotic development. In this article, we explore abandoning the market as a prerequisite for successful antibiotic research and development. Once one stops trying to fix a market model that has stopped functioning, one is free to carry out research and development (R&D) in ways that are more openly collaborative, a mechanism that has been demonstrably effective for the R&D underpinning the response to the COVID pandemic. New "open source" research models have great potential for the development of medicines for areas of public health where the traditional profit-driven model struggles to deliver. New financial initiatives, including major push/pull incentives, aimed at fixing the broken antibiotics market provide one possible means for funding an openly collaborative approach to drug development. We argue that now is therefore the time to evaluate, at scale, whether such methods can deliver new medicines through to patients, in a timely manner.

Functional and Material Properties in Nanocatalyst Design: A Data Handling and Sharing Problem

(1) Background: Properties and descriptors are two forms of molecular in silico representations. Properties can be further divided into functional, e.g., catalyst or drug activity, and material, e.g., X-ray crystal data. Millions of real measured functional property records are available for drugs or drug candidates in online databases. In contrast, there is not a single database that registers a real conversion, TON or TOF data for catalysts. All of the data are molecular descriptors or material properties, which are mainly of a calculation origin. (2) Results: Here, we explain the reason for this. We reviewed the data handling and sharing problems in the design and discovery of catalyst candidates particularly, material informatics and catalyst design, structural coding, data collection and validation, infrastructure for catalyst design and the online databases for catalyst design. (3) Conclusions: Material design requires a property prediction step. This can only be achieved based on the registered real property measurement. In reality, in catalyst design and discovery, we can observe either a severe functional property deficit or even property famine.

Public-Private Partnerships: Compound and Data Sharing in Drug Discovery and Development

Collaborative efforts between public and private entities such as academic institutions, governments, and pharmaceutical companies form an integral part of scientific research, and notable instances of such initiatives have been created within the life science community. Several examples of alliances exist with the broad goal of collaborating toward scientific advancement and improved public welfare. Such collaborations can be essential in catalyzing breaking areas of science within high-risk or global public health strategies that may have otherwise not progressed. A common term used to describe these alliances is public-private partnership (PPP). This review discusses different aspects of such partnerships in drug discovery/development and provides example applications as well as successful case studies. Specific areas that are covered include PPPs for sharing compounds at various phases of the drug discovery process-from compound collections for hit identification to sharing clinical candidates. Instances of PPPs to support better data integration and build better machine learning models are also discussed. The review also provides examples of PPPs that address the gap in knowledge or resources among involved parties and advance drug discovery, especially in disease areas with unfulfilled and/or social needs, like neurological disorders, cancer, and neglected and rare diseases.

Open Innovation in Medical and Pharmaceutical Research: A Literature Landscape Analysis

Open innovation in medical and pharmaceutical research has grown steadily over the last decade. However, the performance of the published literature in terms of the scientific impact and gaining social media attention remains largely unexplored. The scientific literature of open innovation was examined by means of bibliometric analyses to identify the most prolific authors, organizations, countries, journals, research areas, and recurring terms. By accessing the Web of Science Core Collection and Altmetric electronic databases, citation-related and Altmetric data were evaluated. Public-private partnerships and a selection of newly introduced potential novel drugs in the analyzed publications were identified. North America and Europe were the major literature contributors. Research outputs were mainly published in journals focused on business and economics, pharmacology and pharmacy, and engineering. Many pharmaceutical and biotechnological companies contributed to the analyzed publications, with higher mean citation counts and social media attention (Altmetric score) than nonindustry articles. Public-private partnerships fostered financial support, sharing of expertise and intellectual property, and research collaborations. In summary, open innovation might serve as a powerful strategy to both benefit the involved industry entities and accelerate the development of solutions and products for the betterment of human health.

Nonclassical Phenyl Bioisosteres as Effective Replacements in a Series of Novel Open-Source Antimalarials

The replacement of one chemical motif with another that is broadly similar is a common method in medicinal chemistry to modulate the physical and biological properties of a molecule (i.e., bioisosterism). In recent years, bioisosteres such as cubane and bicyclo[1.1.1]pentane (BCP) have been used as highly effective phenyl mimics. Herein, we show the successful incorporation of a range of phenyl bioisosteres during the open-source optimization of an antimalarial series. Cubane (19) and closo-carborane (23) analogues exhibited improved in vitro potency against Plasmodium falciparum compared to the parent phenyl compound; however, these changes resulted in a reduction in metabolic stability; unusually, enzyme-mediated oxidation was found to take place on the cubane core. A BCP analogue (22) was found to be equipotent to its parent phenyl compound and showed significantly improved metabolic properties. While these results demonstrate the utility of these atypical bioisosteres when used in a medicinal chemistry program, the search to find a suitable bioisostere may well require the preparation of many candidates, in our case, 32 compounds.

Open science approaches to COVID-19

In only a matter of months, the coronavirus disease of 2019 (COVID-19) has spread around the world. The global impact of the disease has caused significant and repeated calls for quick action towards new medicines and vaccines. In response, researchers have adopted open science methods to begin to combat this disease via global collaborative efforts. We summarise here some of those initiatives, and have created an updateable list to which others may be added. Though open science has previously been shown as an accelerator of biomedical research, the COVID-19 crisis has made openness seem the logical choice. Will openness persist in the discovery of new medicines, after the crisis has receded?

Anthelmintic drug discovery: target identification, screening methods and the role of open science

Helminths, including cestodes, nematodes and trematodes, are a huge global health burden, infecting hundreds of millions of people. In many cases, existing drugs such as benzimidazoles, diethylcarbamazine, ivermectin and praziquantel are insufficiently efficacious, contraindicated in some populations, or at risk of the development of resistance, thereby impeding progress towards World Health Organization goals to control or eliminate these neglected tropical diseases. However, there has been limited recent progress in developing new drugs for these diseases due to lack of commercial attractiveness, leading to the introduction of novel, more efficient models for drug innovation that attempt to reduce the cost of research and development. Open science aims to achieve this by encouraging collaboration and the sharing of data and resources between organisations. In this review we discuss how open science has been applied to anthelmintic drug discovery. Open resources, including genomic information from many parasites, are enabling the identification of targets for new antiparasitic agents. Phenotypic screening remains important, and there has been much progress in open-source systems for compound screening with parasites, including motility assays but also high content assays with more detailed investigation of helminth physiology. Distributed open science compound screening programs, such as the Medicines for Malaria Venture Pathogen Box, have been successful at facilitating screening in diverse assays against many different parasite pathogens and models. Of the compounds identified so far in these screens, tolfenpyrad, a repurposed insecticide, shows significant promise and there has been much progress in creating more potent and selective derivatives. This work exemplifies how open science approaches can catalyse drug discovery against neglected diseases.

Distributed Manufacturing of Open Source Medical Hardware for Pandemics

Distributed digital manufacturing offers a solution to medical supply and technology shortages during pandemics. To prepare for the next pandemic, this study reviews the state-of-the-art of open hardware designs needed in a COVID-19-like pandemic. It evaluates the readiness of the top twenty technologies requested by the Government of India. The results show that the majority of the actual medical products have some open source development, however, only 15% of the supporting technologies required to produce them are freely available. The results show there is still considerable research needed to provide open source paths for the development of all the medical hardware needed during pandemics. Five core areas of future research are discussed, which include (i) technical development of a wide-range of open source solutions for all medical supplies and devices, (ii) policies that protect the productivity of laboratories, makerspaces, and fabrication facilities during a pandemic, as well as (iii) streamlining the regulatory process, (iv) developing Good-Samaritan laws to protect makers and designers of open medical hardware, as well as to compel those with knowledge that will save lives to share it, and (v) requiring all citizen-funded research to be released with free and open source licenses.

Review on natural products databases: where to find data in 2020

Natural products (NPs) have been the centre of attention of the scientific community in the last decencies and the interest around them continues to grow incessantly. As a consequence, in the last 20 years, there was a rapid multiplication of various databases and collections as generalistic or thematic resources for NP information. In this review, we establish a complete overview of these resources, and the numbers are overwhelming: over 120 different NP databases and collections were published and re-used since 2000. 98 of them are still somehow accessible and only 50 are open access. The latter include not only databases but also big collections of NPs published as supplementary material in scientific publications and collections that were backed up in the ZINC database for commercially-available compounds. Some databases, even published relatively recently are already not accessible anymore, which leads to a dramatic loss of data on NPs. The data sources are presented in this manuscript, together with the comparison of the content of open ones. With this review, we also compiled the open-access natural compounds in one single dataset a COlleCtion of Open NatUral producTs (COCONUT), which is available on Zenodo and contains structures and sparse annotations for over 400,000 non-redundant NPs, which makes it the biggest open collection of NPs available to this date.

KOt-Bu-promoted selective ring-opening N-alkylation of 2-oxazolines to access 2-aminoethyl acetates and N-substituted thiazolidinones

An efficient and simple KOt-Bu-promoted selective ring-opening N-alkylation of 2-methyl-2-oxazoline or 2-(methylthio)-4,5-dihydrothiazole with benzyl halides under basic conditions is described for the first time. The method provides a convenient and practical pathway for the synthesis of versatile 2-aminoethyl acetates and N-substituted thiazolidinones with good functional group tolerance and selectivity. KOt-Bu not only plays an important role to promote this ring-opening N-alkylation, but also acts as an oxygen donor.

Six Laws of Open Source Drug Discovery

Six to swear by! Society needs effective and affordable medicines. We currently have at our disposal essentially one system to discover and develop drugs, and there are many areas where this system struggles to deliver, for example to combat antimicrobial resistance, or tropical diseases, or dementia. It is sensible to cultivate alternative, competing approaches to drug discovery and development. A genuinely new alternative is to open up the entire research cycle, abandoning secrecy altogether. This "open source" approach has now been trialed and the lessons learned distilled to six laws of operation that help to clarify working practices. This article examines and explains those laws, which can be adopted by anyone wishing to create medicines using an inclusive, public process.

Fueling Open Innovation for Malaria Transmission-Blocking Drugs: Hundreds of Molecules Targeting Early Parasite Mosquito Stages

Background

Despite recent successes at controlling malaria, progress has stalled with an estimated 219 million cases and 435,000 deaths in 2017 alone. Combined with emerging resistance to front line antimalarial therapies in Southeast Asia, there is an urgent need for new treatment options and novel approaches to halt the spread of malaria. Plasmodium, the parasite responsible for malaria propagates through mosquito transmission. This imposes an acute bottleneck on the parasite population and transmission-blocking interventions exploiting this vulnerability are recognized as vital for malaria elimination.

Methods

13,533 small molecules with known activity against Plasmodium falciparum asexual parasites were screened for additional transmission-blocking activity in an ex vivo Plasmodium berghei ookinete development assay. Active molecules were then counterscreened in dose response against HepG2 cells to determine their activity/cytotoxicity window and selected non-toxic representative molecules were fully profiled in a range of transmission and mosquito infection assays. Furthermore, the entire dataset was compared to other published screens of the same molecules against P. falciparum gametocytes and female gametogenesis.

Results

437 molecules inhibited P. berghei ookinete formation with an IC₅₀ < 10 μM. of which 273 showed >10-fold parasite selectivity compared to activity against HepG2 cells. Active molecules grouped into 49 chemical clusters of three or more molecules, with 25 doublets and 94 singletons. Six molecules representing six major chemical scaffolds confirmed their transmission-blocking activity against P. falciparum male and female gametocytes and inhibited P. berghei oocyst formation in the standard membrane feeding assay at 1 μM. When screening data in the P. berghei development ookinete assay was compared to published screens of the same library in assays against P. falciparum gametocytes and female gametogenesis, it was established that each assay identified distinct, but partially overlapping subsets of transmission-blocking molecules. However, selected molecules unique to each assay show transmission-blocking activity in mosquito transmission assays.

Conclusion

The P. berghei ookinete development assay is an excellent high throughput assay for efficiently identifying antimalarial molecules targeting early mosquito stage parasite development. Currently no high throughput transmission-blocking assay is capable of identifying all transmission-blocking molecules.

Distributed Biological Foundries for Global Health

Historically, many industries such as manufacturing have undergone a trend away from centralized, large-scale production toward a more distributed form. Currently, this same trend is witnessed in biological manufacturing and bioprocessing, with the rise of biological foundries where one can synthesize, grow, isolate, and purify a broad range of biologics. The adoption of distributed practices for biological processing has significant implications for healthcare, diagnostics, and therapies. This essay discusses the many diverse factors that have facilitated this growth, ranging from the establishment of available biological components, or "parts," low-cost programmable hardware, and others. Currently existing examples of distributed biological foundries are also identified, separating the discussion into those that are accessible only by elite users and the more recent emerging foundries that are more accessible to the general population. Taking lessons from other fields, it is argued that this trend toward distributed biological manufacturing is inevitable, so adapting to this trend is important for the progress of creating new therapeutics, sensors, diagnostics, and reagents for biomedical applications.

Molecular Docking Guided Grid-Independent Descriptor Analysis to Probe the Impact of Water Molecules on Conformational Changes of hERG Inhibitors in Drug Trapping Phenomenon

Human ether a-go-go related gene (hERG) or KV11.1 potassium channels mediate the rapid delayed rectifier current (I_Kr) in cardiac myocytes. Drug-induced inhibition of hERG channels has been implicated in the development of acquired long QT syndrome type (aLQTS) and fatal arrhythmias. Several marketed drugs have been withdrawn for this reason. Therefore, there is considerable interest in developing better tests for predicting drugs which can block the hERG channel. The drug-binding pocket in hERG channels, which lies below the selectivity filter, normally contains K⁺ ions and water molecules. In this study, we test the hypothesis that these water molecules impact drug binding to hERG. We developed 3D QSAR models based on alignment independent descriptors (GRIND) using docked ligands in open and closed conformations of hERG in the presence (solvated) and absence (non-solvated) of water molecules. The ligand–protein interaction fingerprints (PLIF) scheme was used to summarize and compare the interactions. All models delineated similar 3D hERG binding features, however, small deviations of about ~0.4 Å were observed between important hotspots of molecular interaction fields (MIFs) between solvated and non-solvated hERG models. These small changes in conformations do not affect the performance and predictive power of the model to any significant extent. The model that exhibits the best statistical values was attained with a cryo_EM structure of the hERG channel in open state without water. This model also showed the best R² of 0.58 and 0.51 for the internal and external validation test sets respectively. Our results suggest that the inclusion of water molecules during the docking process has little effect on conformations and this conformational change does not impact the predictive ability of the 3D QSAR models.

The past, present and future of anti-malarial medicines

Great progress has been made in recent years to reduce the high level of suffering caused by malaria worldwide. Notably, the use of insecticide-treated mosquito nets for malaria prevention and the use of artemisinin-based combination therapy (ACT) for malaria treatment have made a significant impact. Nevertheless, the development of resistance to the past and present anti-malarial drugs highlights the need for continued research to stay one step ahead. New drugs are needed, particularly those with new mechanisms of action. Here the range of anti-malarial medicines developed over the years are reviewed, beginning with the discovery of quinine in the early 1800s, through to modern day ACT and the recently-approved tafenoquine. A number of new potential anti-malarial drugs currently in development are outlined, along with a description of the hit to lead campaign from which it originated. Finally, promising novel mechanisms of action for these and future anti-malarial medicines are outlined.

Fast-Acting Small Molecules Targeting Malarial Aspartyl Proteases, Plasmepsins, Inhibit Malaria Infection at Multiple Life Stages

The eradication of malaria remains challenging due to the complex life cycle of Plasmodium and the rapid emergence of drug-resistant forms of Plasmodium falciparum and Plasmodium vivax. New, effective, and inexpensive antimalarials against multiple life stages of the parasite are urgently needed to combat the spread of malaria. Here, we synthesized a set of novel hydroxyethylamines and investigated their activities in vitro and in vivo. All of the compounds tested had an inhibitory effect on the blood stage of P. falciparum at submicromolar concentrations, with the best showing 50% inhibitory concentrations (IC₅₀) of around 500 nM against drug-resistant P. falciparum parasites. These compounds showed inhibitory actions against plasmepsins, a family of malarial aspartyl proteases, and exhibited a marked killing effect on blood stage Plasmodium. In chloroquine-resistant Plasmodium berghei and P. berghei ANKA infected mouse models, treating mice with both compounds led to a significant decrease in blood parasite load. Importantly, two of the compounds displayed an inhibitory effect on the gametocyte stages (III-V) of P. falciparum in culture and the liver-stage infection of P. berghei both in in vitro and in vivo. Altogether, our findings suggest that fast-acting hydroxyethylamine-phthalimide analogs targeting multiple life stages of the parasite could be a valuable chemical lead for the development of novel antimalarial drugs.

Open laboratory notebooks: good for science, good for society, good for scientists

The fundamental goal of the growing open science movement is to increase the efficiency of the global scientific community and accelerate progress and discoveries for the common good. Central to this principle is the rapid disclosure of research outputs in open-access peer-reviewed journals and on pre-print servers. The next bold step in this direction is open laboratory notebooks, where research scientists share their research - including detailed protocols, negative and positive results - online and in near-real-time to synergize with their peers. Here, we highlight the benefits of open lab notebooks to science, society and scientists, and discuss the challenges that this nascent movement is facing. We also present the implementation and progress of our own initiative at openlabnotebooks.org, with more than 20 active contributors after one year of operation.

Easy-To-Synthesize Spirocyclic Compounds Possess Remarkable in Vivo Activity against Mycobacterium tuberculosis

Society urgently needs new, effective medicines for the treatment of tuberculosis. To kick-start the required hit-to-lead campaigns, the libraries of pharmaceutical companies have recently been evaluated for starting points. The GlaxoSmithKline (GSK) library yielded many high-quality hits, and the associated data were placed in the public domain to stimulate engagement by the wider community. One such series, the spiro compounds, are described here. The compounds were explored by a combination of traditional in-house research and open source methods. The series benefits from a particularly simple structure and a short associated synthetic chemistry route. Many members of the series displayed striking potency and low toxicity, and highly promising in vivo activity in a mouse model was confirmed with one of the analogues. Ultimately the series was discontinued due to concerns over safety, but the associated data remain public domain, empowering others to resume the series if the perceived deficiencies can be overcome.

Ideation and implementation of an open science drug discovery business model - M4K Pharma

M4K Pharma was incorporated to launch an open science drug discovery program that relies on regulatory exclusivity as its primary intellectual property and commercial asset, in lieu of patents.In many cases and in key markets, using regulatory exclusivity can provide equivalent commercial protection to patents, while also being compatible with open science. The model is proving attractive to government, foundation and individual funders, who collectively have different expectations for returns on investment compared with biotech, pharmaceutical companies, or venture capital investors.In the absence of these investor-driven requirements for returns, it should be possible to commercialize therapeutics at affordable prices.M4K is piloting this open science business model in a rare paediatric brain tumour, but there is no reason it should not be more widely applicable.

Experimentally Validated Pharmacoinformatics Approach to Predict hERG Inhibition Potential of New Chemical Entities

The hERG (human ether-a-go-go-related gene) encoded potassium ion (K⁺) channel plays a major role in cardiac repolarization. Drug-induced blockade of hERG has been a major cause of potentially lethal ventricular tachycardia termed Torsades de Pointes (TdPs). Therefore, we presented a pharmacoinformatics strategy using combined ligand and structure based models for the prediction of hERG inhibition potential (IC₅₀) of new chemical entities (NCEs) during early stages of drug design and development. Integrated GRid-INdependent Descriptor (GRIND) models, and lipophilic efficiency (LipE), ligand efficiency (LE) guided template selection for the structure based pharmacophore models have been used for virtual screening and subsequent hERG activity (pIC₅₀) prediction of identified hits. Finally selected two hits were experimentally evaluated for hERG inhibition potential (pIC₅₀) using whole cell patch clamp assay. Overall, our results demonstrate a difference of less than ±1.6 log unit between experimentally determined and predicted hERG inhibition potential (IC₅₀) of the selected hits. This revealed predictive ability and robustness of our models and could help in correctly rank the potency order (lower μM to higher nM range) against hERG.

An inquiry-based exercise in medicinal chemistry: Synthesis of a molecular library and screening for potential antimalarial and anti-inflammatory compounds

The development of new medicines holds particular fascination for chemistry, biochemistry, and biology students interested in a career in medicine or the life sciences. The identification and refinement of lead compounds to treat diseases requires researchers to be facile in a number of different disciplines including organic synthesis, biochemistry, cell biology, and molecular biology. We have developed an interdisciplinary, inquiry-based laboratory spanning both organic chemistry and biochemistry classes that acquaints students with research in medicinal chemistry. The first part of the exercise takes place in the second semester of organic chemistry, where pairs of students design and execute their own multistep synthesis of a novel compound with anti-inflammatory and/or antimalarial potential. Later, in first semester biochemistry, many of the same students then test these synthesized compounds for cytotoxicity, inhibition of the enzyme nitric oxide synthase, and inhibition of the transcription factor NF-kB. Learning outcomes, measured by the Classroom Undergraduate Research Experience (CURE) survey, suggest that students participating in both classes had higher gains than an average student. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):424-434, 2018.

The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public

NMR is a mature technique that is well established and adopted in a wide range of research facilities from laboratories to hospitals. This accounts for large amounts of valuable experimental data that may be readily exported into a standard and open format. Yet the publication of these data faces an important issue: Raw data are not made available; instead, the information is slimed down into a string of characters (the list of peaks). Although historical limitations of technology explain this practice, it is not acceptable in the era of Internet. The idea of modernizing the strategy for sharing NMR data is not new, and some repositories exist, but sharing raw data is still not an established practice. Here, we present a powerful toolbox built on recent technologies that runs inside the browser and provides a means to store, share, analyse, and interact with original NMR data. Stored spectra can be streamlined into the publication pipeline, to improve the revision process for instance. The set of tools is still basic but is intended to be extended. The project is open source under the Massachusetts Institute of Technology (MIT) licence.

Addressing the most neglected diseases through an open research model: The discovery of fenarimols as novel drug candidates for eumycetoma

Eumycetoma is a chronic infectious disease characterized by a large subcutaneous mass, often caused by the fungus Madurella mycetomatis. A combination of surgery and prolonged medication is needed to treat this infection with a success rate of only 30%. There is, therefore, an urgent need to find more effective drugs for the treatment of this disease. In this study, we screened 800 diverse drug-like molecules and identified 215 molecules that were active in vitro. Minimal inhibitory concentrations were determined for the 13 most active compounds. One of the most potent compounds, a fenarimol analogue for which a large analogue library is available, led to the screening of an additional 35 compounds for their in vitro activity against M. mycetomatis hyphae, rendering four further hit compounds. To assess the in vivo potency of these hit compounds, a Galleria mellonella larvae model infected with M. mycetomatis was used. Several of the compounds identified in vitro demonstrated promising efficacy in vivo in terms of prolonged larval survival and/or reduced fungal burden. The results presented in this paper are the starting point of an Open Source Mycetoma (MycetOS) approach in which members of the global scientific community are invited to participate and contribute as equal partners. We hope that this initiative, coupled with the promising new hits we have reported, will lead to progress in drug discovery for this most neglected of neglected tropical diseases.

Generating Focused Molecule Libraries for Drug Discovery with Recurrent Neural Networks

In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active toward a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against Staphylococcus aureus, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against Plasmodium falciparum (Malaria), it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete de novo drug design cycle to generate large sets of novel molecules for drug discovery.

malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication

Basic science holds enormous power for revealing the biological mechanisms of disease and, in turn, paving the way toward new, effective interventions. Recognizing this power, the 2011 Research Agenda for Malaria Eradication included key priorities in fundamental research that, if attained, could help accelerate progress toward disease elimination and eradication. The Malaria Eradication Research Agenda (malERA) Consultative Panel on Basic Science and Enabling Technologies reviewed the progress, continuing challenges, and major opportunities for future research. The recommendations come from a literature of published and unpublished materials and the deliberations of the malERA Refresh Consultative Panel. These areas span multiple aspects of the Plasmodium life cycle in both the human host and the Anopheles vector and include critical, unanswered questions about parasite transmission, human infection in the liver, asexual-stage biology, and malaria persistence. We believe an integrated approach encompassing human immunology, parasitology, and entomology, and harnessing new and emerging biomedical technologies offers the best path toward addressing these questions and, ultimately, lowering the worldwide burden of malaria.

Plasmodium falciparum in vitro continuous culture conditions: A comparison of parasite susceptibility and tolerance to anti-malarial drugs throughout the asexual intra-erythrocytic life cycle

The continuous culture of Plasmodium falciparum is often seen as a means to an end, that end being to probe the biology of the parasite in question, and ultimately for many in the malaria drug discovery arena, to identify means of killing the parasite in order to treat malaria. In vitro continuous culture of Plasmodium falciparum is a fundamental requirement when undertaking malaria research where the primary objectives utilise viable parasites of a desired lifecycle stage. This investigation, and resulting data, compared the impact culturing Plasmodium falciparum long term (4 months) in different environmental conditions had on experimental outcomes and thus conclusions. The example presented here focused specifically on the effect culture conditions had on the in vitro tolerance of Plasmodium falciparum to standard anti-malarial drugs, including artemisinin and lumefantrine. Historical data from an independent experiment for 3D7-ALB (5% O₂) was also compared with that obtained from this study. We concluded that parasites cultured for several months in media supplemented with a serum substitute such as Albumax II^® or within hyperoxic conditions (21% O₂), demonstrate highly variable responses to artemisinin and lumefantrine but not all anti-malarial drugs, when compared to those cultured in human serum in combination with Albumax II^® under normoxic conditions (5% O₂) for the parasite.

Nitroimidazoles: Molecular Fireworks That Combat a Broad Spectrum of Infectious Diseases

Infectious diseases claim millions of lives every year, but with the advent of drug resistance, therapeutic options to treat infections are inadequate. There is now an urgent need to develop new and effective treatments. Nitroimidazoles are a class of antimicrobial drugs that have remarkable broad spectrum activity against parasites, mycobacteria, and anaerobic Gram-positive and Gram-negative bacteria. While nitroimidazoles were discovered in the 1950s, there has been renewed interest in their therapeutic potential, particularly for the treatment of parasitic infections and tuberculosis. In this review, we summarize different classes of nitroimidazoles that have been described in the literature in the past five years, from approved drugs and clinical candidates to examples undergoing preclinical or early stage development. The relatively "nonspecific" mode of action and resistance mechanisms of nitromidazoles are discussed, and contemporary strategies to facilitate nitroimidazole drug development are highlighted.

An open source pharma roadmap

In an Essay, Matthew Todd and colleagues discuss an open source approach to drug development.