Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions

In silico identification of compounds from Nigella sativa seed oil as potential inhibitors of SARS-CoV-2 targets

BACKGROUND

The growing number of cases, severity and fatality of the COVID-19 pandemic, coupled with the fact that no cure has been found has made infected individuals especially in Africa, to resort to the consumption of different natural products to alleviate their condition. One of such plant materials that have been consumed to remedy the severity of this viral infection is the oil of Nigella sativa seed commonly called black seed oil. In this study, we extracted and characterized the oil from this seed using gas chromatography coupled to a mass selective detector to identify the component phytochemicals. Site-directed multiligand docking of the identified compounds was performed on SARS-CoV-2 molecular targets- Replicase polyprotein 1a, RNA binding protein of NSP9, ADP ribose phosphatase of NSP3, 3-chymotrypsin-like protease 3CLpro, and RNA-dependent RNA polymerase RDRP, and ACE2-angiotensin-converting enzyme from the Homo sapiens.

RESULTS

The binding affinity of caryophyllene oxide was the highest on 3CLpro (- 6.0 kcal/mol), NSP3 (- 6.3 kcal/mol), NSP9 (- 6.3 kcal/mol), and RDRP (- 6.9 kcal/mol) targets, while α-bergamotene gave the best binding affinity on RPIA (5.7 kcal/mol) target. The binding affinity of β-bisabolene on the ACE2 target (- 8.0 kcal/mol) was almost the same as Remdesivir (- 8.1 kcal/mol). The ADMET properties of these three phytochemicals showed that they are good drug leads for these SARS-CoV-2 receptors.

CONCLUSION

The findings from this study strongly indicate that the reported recovery from COVID-19 infection claimed by patients who consumed black seed oil could be linked to the presence of caryophyllene oxide, α-bergamotene, and β-bisabolene in this natural product.

Predicting the bioactivity of 2-alkoxycarbonylallyl esters as potential antiproliferative agents against pancreatic cancer (MiaPaCa-2) cell lines: GFA-based QSAR and ELM-based models with molecular docking

BACKGROUND

The number of cancer-related deaths is on the increase, combating this deadly disease has proved difficult owing to resistance and some serious side effects associated with drugs used to combat it. Therefore, scientists continue to probe into the mechanism of action of cancer cells and designing novel drugs that could combat this disease more safely and effectively. Here, we developed a genetic function approximation model to predict the bioactivity of some 2-alkoxyecarbonyl esters and probed into the mode of interaction of these molecules with an epidermal growth factor receptor (3POZ) using the three-dimensional quantitative structure activity relationship (QSAR), extreme learning machine (ELM), and molecular docking techniques.

RESULTS

The developed QSAR model with predicted (R2pred) of 0.756 showed that the model was fit to be validated parameter for a built model and also proved that the developed model could be used in practical situation, R2 for training set (0.9929) and test set (0.8397) confirmed that the model could successfully predict the activity of new compounds due to its correlation with the experimental activity, the models generated with ELM models showed improved prediction of the activity of the molecules. The lead compounds (22 and 23) had binding energies of -6.327 and -7.232 kcalmol-1 for 22 and 23 respectively and displayed better inhibition at the binding sites of 3POZ when compared with that of the standard drug, chlorambucil (-6.0 kcalmol-1). This could be attributed to the presence of double bonds and the α-ester groups.

CONCLUSION

The QSAR and ELM models had good prognostic ability and could be used to predict the bioactivity of novel anti-proliferative drugs.

Unveiling novel inhibitors of dopamine transporter via in silico drug design, molecular docking, and bioavailability predictions as potential antischizophrenic agents

Background

The inhibition of dopamine transporter is known to play a significant role in the treatment of schizophrenia-related and other mental disorders. In a continuing from our previous study, computational drug design approach, molecular docking simulation, and pharmacokinetics study were explored for the identification of novel inhibitors dopamine transporter as potential Antischizophrenic agents. Consequently, thirteen (13) new inhibitors of dopamine transporter were designed by selecting the molecule with serial number 39 from our previous study as the template molecule because  it exhibits good pharmacological attributes.

Results

Molecular docking simulation results revealed excellent molecular interactions between the protein target (PDB: 4m48) and the ligands (designed inhibitors) with major interactions that involved hydrogen bonding and hydrophobic interactions. Also, some of the designed inhibitors displayed a superior binding affinity range from − 10.0 to − 10.7 kcal/mol compared to the referenced drug (Lumateperone) with a binding affinity of − 9.7 kcal/mol. Computed physicochemical parameters showed that none of the designed inhibitors including the referenced drug violate Lipinski’s rule of five indicating that all the designed inhibitors would be orally bioavailable as potential drug candidates. Similarly, the ADMET/pharmacokinetics evaluations of some designed inhibitors revealed that they possessed good absorption, distribution, metabolism and excretion properties and none of the inhibitors is neither carcinogens nor toxic toward human ether-a-go-go related gene (hERG I) inhibitor or skin sensitization. Likewise, the BOILED-Egg graphics unveils that all the designed inhibitors demonstrate a high probability to be absorbed by the human gastrointestinal tract and could permeate into the brain. Besides, the predicted bioactive parameters suggested that all the selected inhibitors would be active as drug candidates. Furthermore, the synthetic accessibility scores for all the selected inhibitors and referenced drug lied within the easy zone (i.e., between 1–4) with their computed values range from 2.55 to 3.92, this implies that all the selected inhibitors would be very easy to synthesize in the laboratory.

Conclusions

Hence, all the designed inhibitors having shown excellent pharmacokinetics properties and good bioavailabilities attributes with remarkable biochemical interactions could be developed and optimized as novel Antischizophrenic agents after the conclusion of other experimental investigations.

Defining and navigating macrocycle chemical space

Macrocyclic compounds (MCs) are of growing interest for inhibition of challenging drug targets. We consider afresh what structural and physicochemical features could be relevant to the bioactivity of this compound class. Using these features, we performed Principal Component Analysis to map oral and non-oral macrocycle drugs and clinical candidates, and also commercially available synthetic MCs, in structure–property space. We find that oral MC drugs occupy defined regions that are distinct from those of the non-oral MC drugs. None of the oral MC regions are effectively sampled by the synthetic MCs. We identify 13 properties that can be used to design synthetic MCs that sample regions overlapping with oral MC drugs. The results advance our understanding of what molecular features are associated with bioactive and orally bioavailable MCs, and illustrate an approach by which synthetic chemists can better evaluate MC designs. We also identify underexplored regions of macrocycle chemical space.

Macrocyclic compounds (MCs) are of high interest for inhibition of challenging drug targets, but existing oral MC drugs occupy regions of chemical space that are not well sampled by many available synthetic MC chemotypes.

The Discovery of a Novel Antimetastatic Bcl3 Inhibitor

The development of antimetastatic drugs is an urgent healthcare priority for patients with cancer, because metastasis is thought to account for around 90% of cancer deaths. Current antimetastatic treatment options are limited and often associated with poor long-term survival and systemic toxicities. Bcl3, a facilitator protein of the NF-κB family, is associated with poor prognosis in a range of tumor types. Bcl3 has been directly implicated in the metastasis of tumor cells, yet is well tolerated when constitutively deleted in murine models, making it a promising therapeutic target. Here, we describe the identification and characterization of the first small-molecule Bcl3 inhibitor, by using a virtual drug design and screening approach against a computational model of the Bcl3-NF-kB1(p50) protein-protein interaction. From selected virtual screening hits, one compound (JS6) showed potent intracellular Bcl3-inhibitory activity. JS6 treatment led to reductions in Bcl3-NF-kB1 binding, tumor colony formation, and cancer cell migration in vitro; and tumor stasis and antimetastatic activity in vivo, while being devoid of overt systemic toxicity. These results represent a successful application of in silico screening in the identification of protein-protein inhibitors for novel intracellular targets, and confirm Bcl3 as a potential antimetastatic target.

Hydrogel-assisted delivery of lipophilic molecules into aqueous medium for transdermal medication based on environment-specific, regioselective adsorption of graphene oxides

Graphene oxide (GO)-laden agarose composite hydrogels (GOACHs) were utilized to deliver lipophilic molecules from organic to aqueous media without alteration of the lipophilic nature of the molecules and the hydrophilic nature of the GOACHs. After the agarose host networks of the GOACHs were impregnated with the non-polar organic solution of lipophilic molecules via stepwise solvent exchange, their GO guests wielded the edge polar groups to effectively adsorb the lipophilic molecules via hydrogen bonding. After being transferred to aqueous media, the GOACHs were able to not only release the loaded lipophilic molecules but also to adsorb the released lipophilic molecules on the GO non-polar carbon lattice planes via hydrophobic interactions, thus resulting in deliberately balanced release of lipophilic molecules in aqueous media. Based on this environment-specific, regioselective adsorption of their GO guests, the GOACHs were harnessed as carriers for sustained delivery of ibuprofen across rat skin, underpinning their applicability in transdermal medication.

Do Drug-likeness Rules Apply to Oral Prodrugs?

This paper describes a comparative analysis of the physicochemical and structural properties of prodrugs and their corresponding drugs with regard to drug-likeness rules. The dataset used in this work was obtained from the DrugBank. Sixty-five pairs of prodrugs/drugs were retrieved and divided into the following categories: carrier-linked to increase hydrophilic character, carrier-linked to increase absorption, and bioprecursors. We compared the physicochemical properties related to drug-likeness between prodrugs and drugs. Our results show that prodrugs do not always follow Lipinski's Rule of 5, especially as we observed 15 prodrugs with more than 10 hydrogen bond acceptors and 18 with a molecular weight greater than 500 Da. This fact highlights the importance of extending Lipinski's rules to encompass other parameters as both strategies (filtering of drug-like chemical libraries and prodrug design) aim to improve the bioavailability of compounds. Therefore, critical reasoning is fundamental to determine whether a structure has drug-like properties or could be considered a potential orally active compound in the drug-design pipeline.

Quantitation of Cell Membrane Permeability of Cyclic Peptides by Single-Cell Cytoplasm Mass Spectrometry

Cyclic peptides (CPs) have attracted attention as next-generation drugs because they possess both cell-permeable potential as small molecules and specific affinity similar to antibodies. As intracellular molecules are important targets of CPs, quantitation of the intracellular retention and transmembrane permeability of CPs is necessary for drug development. However, permeated CPs within cells cannot be directly assessed by conventional permeability assays using methods such as artificial membranes and cell monolayers. Here, we propose a new approach using single-cell cytoplasm mass spectrometry (SCC-MS). After cells were incubated with CPs, the cytoplasm was directly collected from a single cell using a microneedle followed by nanoelectrospray ionization mass spectrometry detection of the CPs. The height of the CP peak was plotted against time and fitted with a simple function, y = a(1 - e^-bx), to calculate the apparent permeability coefficient (P_app) for both the influx and efflux directions. MCF-7 cells were selected as model cancer cells and cultured with cyclosporin A (CsA) and its demethylated analogs (dmCsA-1, -2, and -3) as model CPs. P_app values (10^-6 cm/s) obtained from cells incubated with 50 μM CPs ranged from 0.017 to 0.121 for influx and 0.20 to 1.48 for efflux. The higher efflux ratio was possibly caused by efflux transporters such as P-glycoprotein, a well-known receptor of CsA. The equilibrated intracellular concentration of CPs was estimated to be as low as 4.1-6.8 μM, which showed good consistency with the high efflux ratio. SCC-MS is promising as a reliable permeability assay for next-generation CP-based pharmaceuticals.

Generative chemistry: drug discovery with deep learning generative models

The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original texts, images, and videos, to the scratching of novel molecular structures the creativity of deep learning generative models exhibits the height machine intelligence can achieve. The purpose of this paper is to review the latest advances in generative chemistry which relies on generative modeling to expedite the drug discovery process. This review starts with a brief history of artificial intelligence in drug discovery to outline this emerging paradigm. Commonly used chemical databases, molecular representations, and tools in cheminformatics and machine learning are covered as the infrastructure for generative chemistry. The detailed discussions on utilizing cutting-edge generative architectures, including recurrent neural network, variational autoencoder, adversarial autoencoder, and generative adversarial network for compound generation are focused. Challenges and future perspectives follow.

Bioactive constituents from Thunbergia erecta as potential anticholinesterase and anti-ageing agents: Experimental and in silico studies

Acetylcholinesterase (AChE) inhibitor and telomerase reverse transcriptase (TERT) potentiator phytochemicals are highly targeted as anti-Alzheimerꞌs disease and as an anti-ageing process. A phytochemical study of Thunbergia erecta aerial parts resulted in the isolation of ten compounds (1-10). Their structures were identified based on spectral data and comparison with literature values. The activity of our pure isolates on AChE and TERT enzymes by documented in vitro assay methods were evaluated. The results indicated that apigenin (2), vanillic acid (4), and acacetin-7-O-β-D-glucoside (7) exhibited potent inhibition of AChE (IC₅₀ 37.33, 30.80 and 49.57 ng/mL, respectively), compared to the standard drug donepezil (IC₅₀ 31.25 ng/mL). In the TERT enzyme assay, compound 7 triggered a 1.66‑fold increase in telomerase activity at the concentration of 2.85 ng/ml. This is the first study that demonstrates that compound 7 isolated from T. erecta can lead to such telomerase activity relative to control cells. Virtual screening studies including docking, rapid overlay chemical structure (ROCS), and calculated structure-property relationships (SPR) were implemented in this work. Molecular docking studies supported the binding of compounds 2, 4, and 7 through hydrogen bonds (HBs) formation to essential amino acid residues namely ARG:24 A, SER:347 A, LYS:51 A, PHE:346 A, and GLY:345 A of acetylcholinesterase. ROCS and SPR analyses realized compound 2 as a possible treatment of Alzheimer's disease and as a lead compound for drug development process through applying semisynthetic modifications.

Concepts for design and analysis of receptor radiopharmaceuticals: The Receptor-Binding Radiotracers series of meetings provided the foundation

A symposium at George Washington University on Receptor-Binding Radiotracers in 1980 and three follow-up meetings held at University of California, San Diego provided a forum for debating the critical concepts involved in the new field of designing and evaluating radiotracers for imaging receptors and transporters. This review is intended to educate young investigators who may be relatively new to receptor radiopharmaceutical development. Our anticipated audience includes researchers in basic pharmacology, radiochemistry, imaging technology and kinetic data analysis and how these disciplines have worked together to build our understanding of the human biology of transporters and receptor signaling in health and disease. We have chosen to focus on radiochemical design of a useful imaging agent and how design is coupled to analysis of data collected from dynamic imaging with that agent. Some pharmacology may be required for designing the imaging agent and some imaging physics may be important in optimizing the quality of data that is collected. However, the key to a successful imaging agent is matching the radiotracer to the target receptor and to analysis of the time-course data that is used to parse delivery from specific binding and subsequent metabolism or degradation. Properly designed imaging agents are providing critical information about human biology in health and disease as well as pharmacodynamic response to drug interventions. The review emphasizes some of the ideas that were controversial at the 1980 conference and chronicles with literature examples how they have resolved over the four decades of using radiotracers to study transporters and receptors in human subjects. These examples show that there are situations where a very small KD, i.e. high affinity, has the potential to yield an image that reflects blood flow more than receptor density. The examples also show that by combining two studies, one with high specific activity and a second with low specific activity injections one can unravel the pseudo-first order rate B'max into the true second-order rate constant, k3, and the unoccupied receptor density. The final section describes how mathematical methods first presented to the receptor-imaging community in 1980 are now being used to provide confidence in the analysis of kinetic biodistribution studies. Our hope is that by bringing these concepts together in a single review, the next generation of scientists developing receptor imaging agents can be much more efficient than their pioneers in developing useful imaging methods.

Telacebec (Q203): Is there a novel effective and safe anti-tuberculosis drug on the horizon?

High prevalence and stronger emergency of various forms of drug-resistant tuberculosis (DR-TB), including the multidrug-resistant (MDR-TB) as well as extensively drug-resistant (XDR-TB) ones, caused by variously resistant Mycobacterium tuberculosis pathogens, make first-line anti-tuberculosis (anti-TB) agents therapeutically more and more ineffective. Therefore, there is an imperative to develop novel highly efficient (synthetic) agents against both drug-sensitive-TB and DR-TB. The exploration of various heterocycles as prospective core scaffolds for the discovery, development and optimization of anti-TB drugs remains an intriguing scientific endeavour. Telacebec (Q203; TCB), a molecule containing an imidazo[1,2-a]pyridine-3-carboxamide (IPA) structural motif, is considered a novel very promising anti-TB agent showing a unique mechanism of action. The compound blocks oxidative phosphorylation by inhibiting a mycobacterial respiratory chain due to interference with a specific cytochrome b subunit (QcrB) of transmembrane bc1 menaquinol-cytochrome c oxidoreductase as an essential component for transporting electrons across the membrane from menaquinol to other specific subunit, cytochrome c (QcrC). Thus, the ability of mycobacteria to synthesize adenosine-5´-triphosphate is limited and energy generating machinery is disabled. The TCB molecule effectively fights drug-susceptible, MDR as well as XDR M. tuberculosis strains. The article briefly explains a mechanism of an anti-TB action related to the compounds containing a variously substituted IPA scaffold and is focused on their fundamental structure-anti-TB activity relationships as well. Special consideration is paid to TCB indicating the importance of particular structural fragments for maintaining (or even improving) favourable pharmacodynamic, pharmacokinetic and/or toxicological properties. High lipophilicity of TCB might be regarded as one of the key physicochemical properties with positive impact on anti-TB effect of the drug. In January 2021, the TCB molecule was also involved in phase-II clinical trials focused on the treatment of Coronavirus Disease-19 caused by Severe Acute Respiratory Syndrome Coronavirus 2.

The application of isatin-based multicomponent-reactions in the quest for new bioactive and druglike molecules

Oxindole derivatives are known for their great interest in the field of Medicinal Chemistry, as they display vast biological activities. Recent efforts concerning the preparation of oxindole derivatives using isatin-based multicomponent reactions (MCRs) constitute a great advance in generating druglike libraries fast and with wide scaffold diversity. In this review, we address those recent developments, exploring the synthetic pathways and biological activities described for these compounds, namely antitumor, antibacterial, antifungal, antiparasitic, antiviral, antioxidant, anti-inflammatory and central nervous system (CNS) pathologies. To add new depth to this work, we used a well-established web-based free tool (SwissADME) to evaluate the most promising scaffolds in what concerns their druglike properties, namely by evaluating their compliance with some of the most valuable rules applied by medicinal chemists in both academia and industrial settings (Lipinski, Ghose, Veber, Egan, Muegge). The aim of this review is to endorse isatin-based MCRs as a valuable synthetic approach to attain new hit compounds bearing the oxindole privileged structure, while critically exploring these scaffolds' druglike properties.

The Potential of Proteolytic Chimeras as Pharmacological Tools and Therapeutic Agents

The induction of protein degradation in a highly selective and efficient way by means of druggable molecules is known as targeted protein degradation (TPD). TPD emerged in the literature as a revolutionary idea: a heterobifunctional chimera with the capacity of creating an interaction between a protein of interest (POI) and a E3 ubiquitin ligase will induce a process of events in the POI, including ubiquitination, targeting to the proteasome, proteolysis and functional silencing, acting as a sort of degradative knockdown. With this programmed protein degradation, toxic and disease-causing proteins could be depleted from cells with potentially effective low drug doses. The proof-of-principle validation of this hypothesis in many studies has made the TPD strategy become a new attractive paradigm for the development of therapies for the treatment of multiple unmet diseases. Indeed, since the initial protacs (Proteolysis targeting chimeras) were posited in the 2000s, the TPD field has expanded extraordinarily, developing innovative chemistry and exploiting multiple degradation approaches. In this article, we review the breakthroughs and recent novel concepts in this highly active discipline.

Application of Advanced Technologies in Natural Product Research: A Review with Special Emphasis on ADMET Profiling

The successful conversion of natural products (NPs) into lead compounds and novel pharmacophores has emboldened the researchers to harness the drug discovery process with a lot more enthusiasm. However, forfeit of bioactive NPs resulting from an overabundance of metabolites and their wide dynamic range have created the bottleneck in NP researches. Similarly, the existence of multidimensional challenges, including the evaluation of pharmacokinetics, pharmacodynamics, and safety parameters, has been a concerning issue. Advancement of technology has brought the evolution of traditional natural product researches into the computer-based assessment exhibiting pretentious remarks about their efficiency in drug discovery. The early attention to the quality of the NPs may reduce the attrition rate of drug candidates by parallel assessment of ADMET profiling. This article reviews the status, challenges, opportunities, and integration of advanced technologies in natural product research. Indeed, emphasis will be laid on the current and futuristic direction towards the application of newer technologies in early-stage ADMET profiling of bioactive moieties from the natural sources. It can be expected that combinatorial approaches in ADMET profiling will fortify the natural product-based drug discovery in the near future.

C-demethylation and 1, 2-amino shift in (E)-2-(1-(3-aminophenyl) ethylidene)hydrazinecarboxamide to (E)-2-(2-aminobenzylidene)hydrazinecarboxamide and their applications

A Novel (E)-2-(1-(3-aminophenyl)ethylidene)hydrazinecarboxamide 1 was synthesized by traditional method and converted to (E)-2-(2-aminobenzylidene)hydrazinecarboxamide 2 by single step in DMSO at room temperature. Synthesized compound 1 was analysed by spectroscopy (NMR and LC–MS) techniques and molecule 2 was characterized using single crystal X-ray diffraction and spectroscopy (NMR and GC–MS) techniques. These analytical technique results revealed that, C-demethylation and 1, 2 amino shift in phenyl ring of compound 1 gives molecule 2. DNA binding studies of compounds 1 and 2 was carried out by electronic absorption spectroscopy. This result revealed that, compounds 1 and 2 showed hyperchromism with bathochromic shift. Anticancer activity of compounds 1 and 2 is carried out by molecular docking with five receptors.Computer aided virtual screening demonstrated that the synthesized molecules possess ideal drug likeliness, pharmacokinetics features, toxicity profile for structure based drug discovery. The molecular docking studies revealed that the synthesized molecules are significant binding with the five selected cancer receptors with minimum binding energy (kcal/mol), number of hydrogen bonds, weak interaction, docking score and cluster RMS. The docking studies also suggested that the molecules showed interactions with DNA and the theoretical values of the binding are comparable with that of the experimental values. Hirshfeld surface analysis was used to analyze and quantify the intermolecular interactions in the crystal structure of compound 2.

Druggability assessment of precursor membrane protein as a target for inhibiting the Zika virus

The Zika virus (ZIKV), a significant zoonotic flavivirus, was neglected as a human pathogen until the recent epidemic. The rapid geographic spread of the virus and association with neurological disorders has created a global public health concern pressing the need for anti-ZIKV drugs. Previous ZIKV drug discovery research has focused on three primary targets, RNA-dependent RNA polymerase, envelope protein, and viral proteases, and none has yet resulted in a commercially viable inhibitor. In the quest for finding effective inhibitors, it is important to expand the number of targets available for drug discovery research. To this end, the ZIKV precursor membrane protein (prM) comes to the forefront as a potential target due to its critical role in virus infectivity and pathogenicity. prM acts as a chaperone for envelope protein folding and prevents premature fusion of virions to the host membrane and has not been attempted as a drug target before. One critical requirement for a protein to be an effective target is the ability of the protein to be druggable, i.e. having active sites that can bind to specific ligands. In this work, the druggability of prM was assessed via molecular docking combined molecular dynamics simulations followed binding affinity kinetics studies. Compounds that had a high affinity to the prM protein were screened in silico and ligand-binding free energies were computed using molecular mechanics with generalized Born and surface area continuum solvation (MM-GBSA) method. In vitro binding kinetics via biolayer interferometry (BLI) and interaction analysis confirmed that prM could be targeted for drug discovery to combat ZIKV infection.Communicated by Ramaswamy H. Sarma.

Handling the Hurdles on the Way to Anti-tuberculosis Drug Development

The global epidemic of tuberculosis (TB) imposes a sustained epidemiologic vigilance and investments in research by governments. Mycobacterium tuberculosis, the main causative agent of TB in human beings, is a very successful pathogen, being the main cause of death in the population among infectious agents. In 2018, ~10 million individuals were contaminated with this bacillus and became ill with TB, and about 1.2 million succumbed to the disease. Most of the success of the M. tuberculosis to linger in the population comes from its ability to persist in an asymptomatic latent state into the host and, in fact, the majority of the individuals are unaware of being contaminated. Even though TB is a treatable disease and is curable in most cases, the treatment is lengthy and laborious. In addition, the rise of resistance to first-line anti-TB drugs elicits a response from TB research groups to discover new chemical entities, preferably with novel mechanisms of action. The pathway to find a new TB drug, however, is arduous and has many barriers that are difficult to overcome. Fortunately, several approaches are available today to be pursued by scientists interested in anti-TB drug development, which goes from massively testing chemical compounds against mycobacteria, to discovering new molecular targets by genetic manipulation. This review presents some difficulties found along the TB drug development process and illustrates different approaches that might be used to try to identify new molecules or targets that are able to impair M. tuberculosis survival.

Water-soluble inhibitors of ABCG2 (BCRP) - A fragment-based and computational approach

A good balance between hydrophilicity and lipophilicity is a prerequisite for all bioactive compounds. If the hydrophilicity of a compound is low, its solubility in water will be meager. Many drug development failures have been attributed to poor aqueous solubility. ABCG2 inhibitors are especially prone to be insoluble since they have to address the extremely large and hydrophobic multidrug binding site in ABCG2. For instance, our previous, tariquidar-related ABCG2 inhibitor UR-MB108 (1) showed high potency (79 nM), but very low aqueous solubility (78 nM). To discover novel potent ABCG2 inhibitors with improved solubility we pursued a fragment-based approach. Substructures of 1 were optimized and the fragments 'enlarged' to obtain inhibitors, supported by molecular docking studies. Synthesis was achieved, i.a., via Sonogashira coupling, click chemistry and amide coupling. A kinetic solubility assay revealed that 1 and most novel inhibitors did not precipitate during the short time period of the applied biological assays. The solubility of the compounds in aqueous media at equilibrium was investigated in a thermodynamic solubility assay, where UR-Ant116 (40), UR-Ant121 (41), UR-Ant131 (48) and UR-Ant132 (49) excelled with solubilities between 1 μM and 1.5 μM - an up to 19-fold improvement compared to 1. Moreover, these novel N-phenyl-chromone-2-carboxamides inhibited ABCG2 in a Hoechst 33342 transport assay with potencies in the low three-digit nanomolar range, reversed MDR in cancer cells, were non-toxic and proved stable in blood plasma. All properties make them attractive candidates for in vitro assays requiring long-term incubation and in vivo studies, both needing sufficient solubility at equilibrium. 41 and 49 were highly ABCG2-selective, a precondition for developing PET tracers. The triple ABCB1/C1/G2 inhibitor 40 qualifies for potential therapeutic applications, given the concerted role of the three transporter subtypes at many tissue barriers, e.g. the BBB.

Evolution of Novartis' Small Molecule Screening Deck Design

This article summarizes the evolution of the screening deck at the Novartis Institutes for BioMedical Research (NIBR). Historically, the screening deck was an assembly of all available compounds. In 2015, we designed a first deck to facilitate access to diverse subsets with optimized properties. We allocated the compounds as plated subsets on a 2D grid with property based ranking in one dimension and increasing structural redundancy in the other. The learnings from the 2015 screening deck were applied to the design of a next generation in 2019. We found that using traditional leadlikeness criteria (mainly MW, clogP) reduces the hit rates of attractive chemical starting points in subset screening. Consequently, the 2019 deck relies on solubility and permeability to select preferred compounds. The 2019 design also uses NIBR's experimental assay data and inferred biological activity profiles in addition to structural diversity to define redundancy across the compound sets.

Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 Mpro, using molecular docking and dynamics simulation studies

Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) Main protease (M^pro) is one of the vital drug targets amongst all the coronaviruses, as the protein is indispensable for virus replication. The study aimed to identify promising lead molecules against M^pro enzyme through virtual screening of Malaria Venture (MMV) Malaria Box (MB) comprising of 400 experimentally proven compounds. The binding affinities were studied using virtual screening based molecular docking, which revealed five molecules having the highest affinity scores compared to the reference molecules. Utilizing the established 3D structure of M^pro the binding affinity conformations of the docked complexes were studied by Molecular Dynamics (MD) simulations. The MD simulation trajectories were analysed to monitor protein deviation, relative fluctuation, atomic gyration, compactness covariance, residue-residue map and free energy landscapes. Based on the present study outcome, we propose three Malaria_box (MB) compounds, namely, MB_241, MB_250 and MB_266 to be the best lead compounds against M^pro activity. The compounds may be evaluated for their inhibitory activities using experimental techniques.

COVID-19: CADD to the rescue

The recent outbreak of the deadly COVID-19 disease, being caused by the novel coronavirus (SARS-CoV-2), has put the world on red alert as it keeps spreading and recording more fatalities. Research efforts are being carried out to curtail the disease from spreading as it has been declared as of global health emergency. Hence, there is an exigent need to identify and design drugs that are capable of curing the infection and hinder its continual spread across the globe. Herein, a computer-aided drug design tool known as the virtual screening method was used to screen a database of 44 million compounds to find compounds that have the potential to inhibit the surface glycoprotein responsible for virus entry and binding. The consensus scoring approach selected three compounds with promising physicochemical properties and favorable molecular interactions with the target protein. These selected compounds can undergo lead optimization to be further developed as drugs that can be used in treating the COVID-19 disease.

Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface

The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional therapeutic modalities are needed to overcome this deficiency. Here, the identification and characterization of a natural product, WDB002, reveals a therapeutic modality that dramatically expands the currently accepted limits of druggability. WDB002, in complex with the FK506-binding protein (FKBP12), potently and selectively binds the human centrosomal protein 250 (CEP250), resulting in disruption of CEP250 function in cells. The recognition mode is unprecedented in that the targeted domain of CEP250 is a coiled coil and is topologically featureless, embodying both a structural motif and surface topology previously considered on the extreme limits of "undruggability" for an intracellular target. Structural studies reveal extensive protein-WDB002 and protein-protein contacts, with the latter being distinct from those seen in FKBP12 ternary complexes formed by FK506 and rapamycin. Outward-facing structural changes in a bound small molecule can thus reprogram FKBP12 to engage diverse, otherwise "undruggable" targets. The flat-targeting modality demonstrated here has the potential to expand the druggable target range of small-molecule therapeutics. As CEP250 was recently found to be an interaction partner with the Nsp13 protein of the SARS-CoV-2 virus that causes COVID-19 disease, it is possible that WDB002 or an analog may exert useful antiviral activity through its ability to form high-affinity ternary complexes containing CEP250 and FKBP12.

Molecular docking, ADMET study and in vivo pharmacological research of N-(3,4-dimetoxyphenyl)-2-{[2-methyl-6-(pyridine-2-yl)-pyrimidin-4-yl]thio}acetamide as a promising anticonvulsant

Introduction: The search for new anticonvulsants for epilepsy treatment with higher efficacy and better tolerability remains important. The aim of the present research was an in silico and in vivo pharmacological study of N-(3,4-dimethoxyphenyl)-2-((2-methyl-6-(pyridin-2-yl)pyrimidin-4-yl)thio)acetamide (Epirimil) as a promising anticonvulsant.

Materials and methods: A 1H and 13C NMR spectroscopy, LS/MS, and an elemental analysis were used to determine Epirimil structure. An ADMET analysis, as well as a docking study using anticonvulsant biotargets, e.g.: GABAAR, GABAAT, CA II, NMDAR, and AMPAR, was carried out. Anticonvulsant activity was proved, using PTZ- and MES-induced seizures in rats and mice, and neurotoxicity was determined using a rotarod test. Influence of Epirimil on the psycho-emotional state of the laboratory animals was determined by an open field test.

Results and discussion: A synthesis method of a promising anticonvulsant Epirimil was modified. The calculated ADMET parameters and a molecular docking into the active sites of anticonvulsant biotargets allowed evaluating the research prospects and predicting possible mechanisms for implementing anticonvulsant activity. A prominent anticonvulsant activity of Epirimil was established using in vivo studies on the model of PTZ-induced seizures in rats and MES-induced seizures in mice. In terms of toxicity, Epirimil belongs to class IV – low toxic substances. The open field test showed that Epirimil had almost no effect on the animals’ behavioral responses: it neither changed their psycho-emotional activity, nor increased their anxiety level. ED50, TD50 and protective index of Epirimil according to its anticonvulsant activity were calculated.

Conclusion: The obtained experimental results substantiate the prospects of N-(3,4-Dimethoxyphenyl)-2-((2-methyl-6-(pyridin-2-yl)pyrimidin-4-yl)thio)acetamide as a promising active pharmaceutical ingredient having a multifactor mechanism of anticonvulsant activity.

Graphical abstract

Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches

Recently, there has been increased interest in aminoacyl tRNA synthetases (aaRSs) as potential malarial drug targets. These enzymes play a key role in protein translation by the addition of amino acids to their cognate tRNA. The aaRSs are present in all Plasmodium life cycle stages, and thus present an attractive malarial drug target. Prolyl tRNA synthetase is a class II aaRS that functions in charging tRNA with proline. Various inhibitors against Plasmodium falciparum ProRS (PfProRS) active site have been designed. However, none have gone through clinical trials as they have been found to be highly toxic to human cells. Recently, a possible allosteric site was reported in PfProRS with two possible allosteric modulators: glyburide and TCMDC-124506. In this study, we sought to identify novel selective inhibitors targeting PfProRS active site and possible novel allosteric modulators of this enzyme. To achieve this, virtual screening of South African natural compounds against PfProRS and the human homologue was carried out using AutoDock Vina. The modulation of protein motions by ligand binding was studied by molecular dynamics (MD) using the GROningen MAchine for Chemical Simulations (GROMACS) tool. To further analyse the protein global motions and energetic changes upon ligand binding, principal component analysis (PCA), and free energy landscape (FEL) calculations were performed. Further, to understand the effect of ligand binding on the protein communication, dynamic residue network (DRN) analysis of the MD trajectories was carried out using the MD-TASK tool. A total of ten potential natural hit compounds were identified with strong binding energy scores. Binding of ligands to the protein caused observable global and residue level changes. Dynamic residue network calculations showed increase in betweenness centrality (BC) metric of residues at the allosteric site implying these residues are important in protein communication. A loop region at the catalytic domain between residues 300 and 350 and the anticodon binding domain showed significant contributions to both PC1 and PC2. Large motions were observed at a loop in the Z-domain between residues 697 and 710 which was also in agreement with RMSF calculations that showed increase in flexibility of residues in this region. Residues in this loop region are implicated in ATP binding and thus a change in dynamics may affect ATP binding affinity. Free energy landscape (FEL) calculations showed that the holo protein (protein-ADN complex) and PfProRS-SANC184 complexes were stable, as shown by the low energy with very few intermediates and hardly distinguishable low energy barriers. In addition, FEL results agreed with backbone RMSD distribution plots where stable complexes showed a normal RMSD distribution while unstable complexes had multimodal RMSD distribution. The betweenness centrality metric showed a loss of functional importance of key ATP binding site residues upon allosteric ligand binding. The deep basins in average L observed at the allosteric region imply that there is high accessibility of residues at this region. To further analyse BC and average L metrics data, we calculated the ΔBC and ΔL values by taking each value in the holo protein BC or L matrix less the corresponding value in the ligand-bound complex BC or L matrix. Interestingly, in allosteric complexes, residues located in a loop region implicated in ATP binding had negative ΔL values while in orthosteric complexes these residues had positive ΔL values. An increase in contact frequency between residues Ser263, Thr267, Tyr285, and Leu707 at the allosteric site and residues Thr397, Pro398, Thr402, and Gln395 at the ATP binding TXE loop was observed. In summary, this study identified five potential orthosteric inhibitors and five allosteric modulators against PfProRS. Allosteric modulators changed ATP binding site dynamics, as shown by RMSF, PCA, and DRN calculations. Changes in dynamics of the ATP binding site and increased contact frequency between residues at the proposed allosteric site and the ATP binding site may explain how allosteric modulators distort the ATP binding site and thus might inhibit PfProRS. The scaffolds of the identified hits in the study can be used as a starting point for antimalarial inhibitor development with low human cytotoxicity.

Druggability and drug-likeness concepts in drug design: are biomodelling and predictive tools having their say?

The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various identified disease targets, in addition to other challenges. Likewise, the high attrition rate of drug candidates in the drug discovery process has also become an enormous challenge for the pharmaceutical industry. To alleviate this negative outlook, new trends in drug discovery have emerged. By drifting away from experimental research methods, computational tools and big data are becoming valuable in the prediction of biological target druggability and the drug-likeness of potential therapeutic agents. These tools have proven to be useful in saving time and reducing research costs. As with any emerging technique, however, controversial opinions have been presented regarding the validation of predictive computational tools. To address the challenges associated with these varying opinions, this review attempts to highlight the principles of druggability and drug-likeness and their recent advancements in the drug discovery field. Herein, we present the different computational tools and their reliability of predictive analysis in the drug discovery domain. We believe that this report would serve as a comprehensive guide towards computational-oriented drug discovery research. Graphical abstract Highlights of methods for assessing the druggability of biological targets.

Cheminformatics Analysis and Modeling with MacrolactoneDB

Macrolactones, macrocyclic lactones with at least twelve atoms within the core ring, include diverse natural products such as macrolides with potent bioactivities (e.g. antibiotics) and useful drug-like characteristics. We have developed MacrolactoneDB, which integrates nearly 14,000 existing macrolactones and their bioactivity information from different public databases, and new molecular descriptors to better characterize macrolide structures. The chemical distribution of MacrolactoneDB was analyzed in terms of important molecular properties and we have utilized three targets of interest (Plasmodium falciparum, Hepatitis C virus and T-cells) to demonstrate the value of compiling this data. Regression machine learning models were generated to predict biological endpoints using seven molecular descriptor sets and eight machine learning algorithms. Our results show that merging descriptors yields the best predictive power with Random Forest models, often boosted by consensus or hybrid modeling approaches. Our study provides cheminformatics insights into this privileged, underexplored structural class of compounds with high therapeutic potential.

SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides

We report on a new cheminformatics enumeration technology—SIME, synthetic insight-based macrolide enumerator—a new and improved software technology. SIME can enumerate fully assembled macrolides with synthetic feasibility by utilizing the constitutional and structural knowledge extracted from biosynthetic aspects of macrolides. Taken into account by the software are key information such as positions in macrolide structures at which chemical components can be inserted, and the types of structural motifs and sugars of interest that can be synthesized and incorporated at those positions. Additionally, we report on the chemical distribution analysis of the newly SIME-generated V1B (virtual 1 billion) library of macrolides. Those compounds were built based on the core of the Erythromycin structure, 13 structural motifs and a library of sugars derived from eighteen bioactive macrolides. This new enumeration technology can be coupled with cheminformatics approaches such as QSAR modeling and molecular docking to aid in drug discovery for rational designing of next generation macrolide therapeutics with desirable pharmacokinetic properties.

Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation

HDAC6 regulates the expression and activity of various tumor-related proteins, but currently there is no selective inhibitor targeting HDAC6 for clinical application. In order to discover novel HDAC6 inhibitors, virtual screening methods comprised of pharmacophore based virtual screening, molecular docking and molecular dynamics (MD) simulations were employed. 15 molecules were obtained after virtual screening. After in vitro bioassays, two of the hits showed inhibition activity against HDAC6, among which the inhibition activity of G1 to HDAC6 reached 81% at concentration of 20 μM. In addition, the inhibitory activity against HDAC1 and HDAC10 demonstrated that G1 and G10 were highly selective to HDAC6. The analysis of the binding modes of G1 and G10 provides a reference for further development of highly active HDAC6 inhibitors. Communicated by Ramaswamy H. Sarma.

Exploring the ring potential of 2,4-diaminopyrimidine derivatives towards the identification of novel caspase-1 inhibitors in Alzheimer's disease therapy

Pro-inflammatory activation of caspase-1 in the neurodegenerative pathway has been associated with age-dependent cognitive impairment and Alzheimer's disease (AD) in humans. A recent report highlighted 2,4-diaminopyrimidine ring as an essential fragment in the inhibition of human caspase-1. However, the role of the ring and its enzyme inhibitory mechanism is not thoroughly investigated at the molecular level. The purpose of this study is therefore in twofold: (1) to understand the enzyme binding mechanism of the 2,4-diaminopyrimidine ring and (2) to search for more potent caspase-1 inhibitors that contain the ring, using integrative per-residue energy decomposition (PRED) pharmacophore modeling. Ligand interaction profile of a reference compound revealed a peculiar hydrogen formation of the amino group of 2,4-diaminopyrimidine with active site residue Arg341, possibly forming the bases for its inhibitory prowess against caspase-1. A generated pharmacophore model for structure-based virtual screening identified compounds, ZINC724667, ZINC09908119, and ZINC09933770, as potential caspase-1 inhibitors that possessed desirable pharmacokinetic and physiochemical properties. Further analyses revealed active site residues, Arg179, Ser236, Cys285, Gln283, Ser339, and Arg341, as crucial to inhibitor binding by stabilizing and forming hydrogen bonds, hydrophobic, and pi-pi interactions with the 2,4-diaminopyrimidine rings. Common interaction patterns of the hits could have accounted for their selective and high-affinity ligand binding, which was characterized by notable disruptions in caspase-1 structural architecture. These compounds could further be explored as potential leads in the development of novel caspase-1 inhibitors.

Structural, biological and pharmaceutical importance of antibiotic agent chloramphenicol

The vibrational, magnetic resonance and electronic spectral techniques are used to evaluate structural activity associated physico-chemical properties. The biological affinity and drug importance was validated by calculating biological parameters using HyperChem. Mulliken charge assignment for restoring chemical potential for generating drug potential in the molecular site was mapped and analyzed. The vibrational spectral pattern was estimated by identifying active and inactive bands and hindrance of vibrational activity of Acetamide group was monitored and thereby drug malfunction was tested. The chemical reaction pathway around the core carbons of chain and ring was keenly noted and the cause of chemical potential for the inducement of drug mechanism was reported. The stimulation of chemical mechanism for antibiotic activity was addressed by suitable evidence and further improvement for enhancing activity was made. The electronic HOMO and LUMO interaction over different molecular entities are discussed to expose accompany of drug mechanical transitions. The CT complex was recognized to be C=N and C=C bonds and operating drug mechanism was monitored. The unwanted drug property induced by perplexes of charge depletion on α-hydroxyl group was assessed from MEP map. The hyperactive polarization energy of 266.18 X10-33 esu and 327 X10-33 esu of present compound is causing biological activity in good order. The uncontrolled breathing region of Acetamide group was clarified in VCD profile and this is main cause to produce toxicity in drug process.

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models

Tubercular Mycobacteria and Legionella pneumophila are the causative agents of potentially fatal respiratory diseases due to their intrinsic pathogenesis but also due to the emergence of antibiotic resistance that limits treatment options. The aim of our study was to explore the antimicrobial activity of a small ligand-based chemical library of 1255 structurally diverse compounds. These compounds were screened in a combination of three assays, two monitoring the intracellular growth of the pathogenic bacteria, Mycobacterium marinum and L. pneumophila, and one assessing virulence of M. marinum. We set up these assays using two amoeba strains, the genetically tractable social amoeba Dictyostelium discoideum and the free-living amoeba Acanthamoeba castellanii. In summary, 64 (5.1%) compounds showed anti-infective/anti-virulence activity in at least one of the three assays. The intracellular assays hit rate varied between 1.7% (n = 22) for M. marinum and 2.8% (n = 35) for L. pneumophila with seven compounds in common for both pathogens. In parallel, 1.2% (n = 15) of the tested compounds were able to restore D. discoideum growth in the presence of M. marinum spiked in a lawn of food bacteria. We also validated the generality of the hits identified in the A. castellanii–M. marinum anti-infective screen using the D. discoideum–M. marinum host–pathogen model. The characterization of anti-infective and antibacterial hits in the latter infection model revealed compounds able to reduce intracellular growth more than 50% at 30 μM. Moreover, the chemical space and physico-chemical properties of the anti-M. marinum hits were compared to standard and candidate Mycobacterium tuberculosis (Mtb) drugs using ChemGPS-NP. A principle component analysis identified separate clusters for anti-M. marinum and anti-L. pneumophila hits unveiling the potentially new physico-chemical properties of these hits compared to standard and candidate M. tuberculosis drugs. Our studies underscore the relevance of using a combination of low-cost and low-complexity assays with full 3R compliance in concert with a rationalized focused library of compounds to identify new chemical scaffolds and to dissect some of their properties prior to taking further steps toward compound development.

Traditional Chinese medicine extraction method by ethanol delivers drug-like molecules

Traditional Chinese Medicine (TCM) is an important reservoir for bioactive natural products. TCM extraction methods by water decoction and wine tincture are an integral part of TCM and essential for their widely acknowledged efficacy. In this study, we selected 6 common TCMs that are rich in chemistry to investigate whether the TCM extraction methods deliver molecules with drug-like physical chemical properties. Six TCM herbal materials were extracted by water, 95% ethanol, and sequential hexane, dichloromethane and methanol. The extracts were analyzed by HPLC and ¹H NMR. Isolation on one of the extracts yielded 32 compounds, their physical chemical properties were analyzed by Instant JChem. Our results showed that ethanol extraction, which mimics TCM wine tincture, delivered compounds with physical chemical properties compliant to Lipinski's rule of 5.

Striking essential oil: tapping into a largely unexplored source for drug discovery

Essential oils (EOs) have been used therapeutically for centuries. In recent decades, randomized controlled (clinical) trials have supported efficacy in specific therapeutic indications for a few of them. Some EOs, their components or derivatives thereof have been approved as drugs. Nevertheless, they are still considered products that are mainly used in complementary and alternative medicine. EO components occupy a special niche in chemical space, that offers unique opportunities based on their unusual physicochemical properties, because they are typically volatile and hydrophobic. Here we evaluate selected physicochemical parameters, used in conventional drug discovery, of EO components present in a range of commercially available EOs. We show that, contrary to generally held belief, most EO components meet current-day requirements of medicinal chemistry for good drug candidates. Moreover, they also offer attractive opportunities for lead optimization or even fragment-based drug discovery. Because their therapeutic potential is still under-scrutinized, we propose that this be explored more vigorously with present-day methods.

Contributions of natural products to ion channel pharmacology

Covering: Up to 2020Ion channels are a vast super-family of membrane proteins that play critical physiological roles in excitable and non-excitable cells. Their biomedical importance makes them valuable and attractive drug targets for neurological, cardiovascular, gastrointestinal and metabolic diseases, and for cancer therapy and immune modulation. Current therapeutics target only a minor subset of ion channels, leaving a large unexploited space within the ion channel field. Natural products harnessed from the almost unlimited and diverse universe of compounds within the bioenvironment have been used to modulate channels for decades. In this review we highlight the impact made by natural products on ion channel pharmacology, specifically on K⁺, Na_V and Ca_V channels, and use case studies to describe the development of ion channel-modulating drugs from natural sources for the treatment of pain, heart disease and autoimmune diseases.

Molecular and Crystal Features of Thermostable Energetic Materials: Guidelines for Architecture of "Bridged" Compounds

Extensive density functional theory (DFT) calculation and data analysis on molecular and crystal level features of 60 reported energetic materials (EMs) allowed us to define key descriptors that are characteristics of these compounds' thermostability. We see these descriptors as reminiscent of "Lipinski's rule of 5", which revolutionized the design of new orally active pharmaceutical molecules. The proposed descriptors for thermostable EMs are of a type of molecular design, location and type of the weakest bond in the energetic molecule, as well as specific ranges of oxygen balance, crystal packing coefficient, Hirshfeld surface hydrogen bonding, and crystal lattice energy. On this basis, we designed three new thermostable EMs containing bridged, 3,5-dinitropyrazole moieties, HL3, HL7, and HL9, which were synthesized, characterized, and evaluated in small-scale field detonation experiments. The best overall performing compound HL7 exhibited an onset decomposition temperature of 341 °C and has a density of 1.865 g cm-3, and the calculated velocity of detonation and maximum detonation pressure were 8517 m s-1 and 30.6 GPa, respectively. Considering HL7's impressive safety parameters [impact sensitivity (IS) = 22 J; friction sensitivity (FS) = 352; and electrostatic discharge sensitivity (ESD) = 1.05 J] and the results of small-scale field detonation experiments, the proposed guidelines should further promote the rational design of novel thermostable EMs, suitable for deep well drilling, space exploration, and other high-value defense and civil applications.

Impact of the chemical structure on the distribution of neuroprotective N-alkyl-9H-carbazoles at octanol/water interfaces

All-atom molecular dynamics (MD) simulations were performed on distribution and agglomeration dynamics of neuroprotective N-(3-anilinopropyl)-9H-carbazoles at octanol/water interfaces.

Potential Therapeutic Approaches to Alzheimer's Disease By Bioinformatics, Cheminformatics And Predicted Adme-Tox Tools

BACKGROUND

Alzheimer's disease (AD) is considered a severe, irreversible and progressive neurodegenerative disorder. Currently, the pharmacological management of AD is based on a few clinically approved acethylcholinesterase (AChE) and N-methyl-D-aspartate (NMDA) receptor ligands, with unclear molecular mechanisms and severe side effects.

METHODS

Here, we reviewed the most recent bioinformatics, cheminformatics (SAR, drug design, molecular docking, friendly databases, ADME-Tox) and experimental data on relevant structurebiological activity relationships and molecular mechanisms of some natural and synthetic compounds with possible anti-AD effects (inhibitors of AChE, NMDA receptors, beta-secretase, amyloid beta (Aβ), redox metals) or acting on multiple AD targets at once. We considered: (i) in silico supported by experimental studies regarding the pharmacological potential of natural compounds as resveratrol, natural alkaloids, flavonoids isolated from various plants and donepezil, galantamine, rivastagmine and memantine derivatives, (ii) the most important pharmacokinetic descriptors of natural compounds in comparison with donepezil, memantine and galantamine.

RESULTS

In silico and experimental methods applied to synthetic compounds led to the identification of new AChE inhibitors, NMDA antagonists, multipotent hybrids targeting different AD processes and metal-organic compounds acting as Aβ inhibitors. Natural compounds appear as multipotent agents, acting on several AD pathways: cholinesterases, NMDA receptors, secretases or Aβ, but their efficiency in vivo and their correct dosage should be determined.

CONCLUSION

Bioinformatics, cheminformatics and ADME-Tox methods can be very helpful in the quest for an effective anti-AD treatment, allowing the identification of novel drugs, enhancing the druggability of molecular targets and providing a deeper understanding of AD pathological mechanisms.

Rationalization of a traditional liver medicine using systems biology approach and its evaluation in preclinical trial

'Bottom-up', i.e., molecule to medicine strategy for the discovery of new drugs takes enormous time and cost. In most of the cases, inherent toxicity and undesired side effects of the developed drug hinder its way beyond the early stages of development. In this regard, the systems pharmacology can play an excellent role by reducing the cost and time of drug development through rationalization and/or repurposing of traditional drugs with known side effects. In the present study, our aim was to develop an integrated systems biology method for the prediction of active ingredients of a traditional medicine and their potential targets inside the body. Further, we evaluated the predictive capacity of the developed method in a preclinical animal model. Here, we have prepared a formulation (SKP17LIV01) from an extract of eight medicinal plants traditionally used as liver medicine and identified the constituents using UHPLC-MS technique. Using systems biology approach, we have rationalized the components of the formulation for potential use in the treatment of heavy metal-induced hepatotoxicity. The active ingredients and potential therapeutic targets were also predicted. A detailed biochemical, histopathological and molecular study on the mice model of lead toxicity confirms the efficacy of the formulation as per prediction by the systems pharmacology approach. The study may open a new frontier for re-discovery of drugs that are already used in traditional medicine.

o-Hydroxycinnamic derivatives as prospective anti-platelet candidates: in silico pharmacokinetic screening and evaluation of their binding sites on COX-1 and P2Y12 receptors

Background The high prevalence of thrombotic abnormalities has become a major concern in the health sector. This is triggered by uncontrolled platelet aggregation, which causes complications and death. The problem becomes more complicated because of the undesirable side effects of the drugs currently in use, some of which have reportedly become resistant. This study aims to evaluate the potency of o-hydroxycinnamic acid derivatives (OCA1a-22a) and their pharmacokinetic properties and toxicity for them to be developed as new antiplatelet candidates. Methods In silico analysis of pharmacokinetics was carried out using pKCSM. Molecular docking of the compounds OCA 1a-22a was performed using the Molegro Virtual Docker. In silico evaluation of the potency of biological activity was done by measuring the bonding energy of each tested compound to the target receptor i.e. COX-1 and P2Y12, as the Moldock score (MDS). Results pKCSM analyses showed that more than 90% of OCA 1a-22a are absorbed through the intestine and distributed in plasma. Most tested compounds are not hepatotoxic, and none is mutagenic. An evaluation of the COX-1 receptor showed that OCA 2a-22a have lower binding energy compared to aspirin, which is the COX-1 inhibitor used today. So, it can be predicted that OCA 2-22a have stronger activity. Interactions with P2Y12 show lower MDS than aspirin, but slightly higher than ibuprofen, which is the standard ligand. Conclusions ADMET (absorption, distribution, metabolism, excretion, and toxicity) profile prediction shows that OCA 1a-22a have the potential to be developed as oral preparations. OCA 1a-22a have strong potential to interact with COX-1 and P2Y12 receptors, so they are prospective anti-platelet candidates.

Synthesis of novel 2-pyrrolidinone and pyrrolidine derivatives and study of their inhibitory activity against autotaxin enzyme

Autotaxin (ATX), a glycoprotein (~125 kDa) isolated as an autocrine motility factor from melanoma cells, belongs to a seven-membered family of ectonucleotide pyrophosphatase/phosphodiesterase (ENPP), and exhibits lysophospholipase D activity. ATX is responsible for the hydrolysis of lysophosphatidylcholine (LPC) to produce the bioactive lipid lysophosphatidic acid (LPA), which is upregulated in a variety of pathological inflammatory conditions, including fibrosis, cancer, liver toxicity and thrombosis. Given its role in human disease, the ATX-LPA axis is an interesting target for therapy, and the development of novel potent ATX inhibitors is of great importance. In the present work a novel class of ATX inhibitors, optically active derivatives of 2-pyrrolidinone and pyrrolidine heterocycles were synthesized. Some of them exhibited interesting in vitro activity, namely the hydroxamic acid 16 (IC₅₀ 700 nM) and the carboxylic acid 40b (IC₅₀ 800 nM), while the boronic acid derivatives 3k (IC₅₀ 50 nM), 3l (IC₅₀ 120 nM), 3 m (IC₅₀ 180 nM) and 21 (IC₅₀ 35 nM) were found to be potent inhibitors of ATX.

Medicines discovery for auditory disorders: Challenges for industry

Currently, no approved medicines are available for the prevention or treatment of hearing loss. Pharmaceutical industry productivity across all therapeutic indications has historically been disappointing, with a 90% chance of failure in delivering a marketed drug after entering clinical evaluation. To address these failings, initiatives have been applied in the three cornerstones of medicine discovery: target selection, clinical candidate selection, and clinical studies. These changes aimed to enable data-informed decisions on the translation of preclinical observations into a safe, clinically effective medicine by ensuring the best biological target is selected, the most appropriate chemical entity is advanced, and that the clinical studies enroll the correct patients. The specific underlying pathologies need to be known to allow appropriate patient selection, so improved diagnostics are required, as are methodologies for measuring in the inner ear target engagement, drug delivery and pharmacokinetics. The different therapeutic strategies of protecting hearing or preventing hearing loss versus restoring hearing are reviewed along with potential treatments for tinnitus. Examples of current investigational drugs are discussed to highlight key challenges in drug discovery and the learnings being applied to improve the probability of success of launching a marketed medicine.

The Symbiotic Relationship Between Drug Discovery and Organic Chemistry

All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.