In Silico Docking of Medicinal Herbs Against P. gingivalis for Chronic Periodontitis Intervention

OBJECTIVE

This study aimed to explore the therapeutic potential of medicinal herbs for chronic periodontitis by examining the molecular interactions between specific herbal compounds and the heme-binding protein of Porphyromonas gingivalis, a key pathogen involved in the disease.

METHODS

The crystal structure of heme-binding protein was obtained from the Protein Data Bank. Herbal compounds were identified through an extensive literature review. Molecular docking simulations were performed to predict binding affinities, followed by Absorption, Distribution, Metabolism, and Excretion (ADME) parameter prediction. Drug-likeness was assessed based on Lipinski's Rule of Five, and pharmacophore modeling was conducted to identify key molecular interactions.

RESULTS

The molecular docking simulations revealed that chelidonine, rotenone, and myricetin exhibited significant binding affinities to the heme-binding protein, with docking scores of -6.5 kcal/mol, -6.4 kcal/mol, and -6.1 kcal/mol, respectively. These compounds formed stable interactions with key amino acid residues within the binding pocket. ADME analysis indicated that all 3 compounds had favourable pharmacokinetic properties, with no violations of Lipinski's rules and minimal predicted toxicity. Pharmacophore modeling further elucidated the interaction profiles, highlighting specific hydrogen bonds and hydrophobic interactions critical for binding efficacy.

CONCLUSIONS

Chelidonine, rotenone, and myricetin emerged as promising therapeutic candidates for chronic periodontitis due to their strong binding affinities, favorable ADME profiles, and lack of significant toxicity. The detailed pharmacophore modeling provided insights into the molecular mechanisms underpinning their inhibitory effects on the heme-binding protein of P. gingivalis. These findings suggest that these compounds have the potential for further development as effective treatments for chronic periodontitis. Future research should focus on in vitro and in vivo validation of these findings to confirm the efficacy and safety of these compounds in biological systems.

ResBiGAAT: Residual Bi-GRU with attention for protein-ligand binding affinity prediction

Protein-ligand interaction plays a crucial role in drug discovery, facilitating efficient drug development and enabling drug repurposing. Several computational algorithms, such as Graph Neural Networks and Convolutional Neural Networks, have been proposed to predict the binding affinity using the three-dimensional structure of ligands and proteins. However, there are limitations due to the need for experimental characterization of the three-dimensional structure of protein sequences, which is still lacking for some proteins. Moreover, these models often suffer from unnecessary complexity, resulting in extraneous computations. This study presents ResBiGAAT, a novel deep learning model that combines a deep Residual Bidirectional Gated Recurrent Unit with two-sided self-attention mechanisms. ResBiGAAT leverages protein and ligand sequence-level features and their physicochemical properties to efficiently predict protein-ligand binding affinity. Through rigorous evaluation using 5-fold cross-validation, we demonstrate the performance of our proposed approach. The model exhibits competitive performance on an external dataset, highlighting its generalizability. Our publicly available web interface, located at resbigaat.streamlit.app, allows users to conveniently input protein and ligand sequences to estimate binding affinity.

Design, synthesis, electrochemistry and anti-trypanosomatid hit/lead identification of nitrofuranylazines

Chagas disease and leishmaniasis are vector-borne infectious diseases affecting both humans and animals. These neglected tropical diseases can be fatal if not treated. Hundreds to thousands of new Chagas disease and leishmaniasis cases are being reported by the WHO every year, and currently available treatments are insufficient. Severe adverse effects, impractical administrations and increased pathogen resistance against current clinical treatments underscore a serious need for the development of new drugs to curb these ailments. In search for such drugs, we investigated a series of nitrofuran-based azine derivatives. Herein, we report the design, synthesis, electrochemistry, and biological activity of these derivatives against promastigotes and amastigotes of Leishmania major, and L. donovani strains, as well as epimastigotes and trypomastigotes of Trypanosoma cruzi. Two leishmanicidal early leads and one trypanosomacidal hit with submicromolar activity were uncovered and stand for further in vivo investigation in the search for new antitrypanosomatid drugs. Future objective will focus on the identification of involved biological targets with the parasites.

Current screening, design, and delivery approaches to address low permeability of chemically synthesized modalities in drug discovery and early clinical development

A drug's permeability across biological membranes is a key property associated with the successful development of an orally absorbed drug candidate. Although a variety of methods are available for predicting and assessing permeability, some are more preferred than others at specific stages of drug discovery and development across the pharmaceutical industry. Permeability measurements may be interpreted differently depending on the chosen method. Herein, we present a refreshed perspective on the screening approaches and philosophy in permeability evaluation, from early drug discovery to early clinical development. Additionally, we review and discuss chemical design and drug delivery technologies that can be leveraged to overcome permeability challenges, which are increasingly being used with emerging modalities.

Challenges and opportunities in delivering oral peptides and proteins

INTRODUCTION

Rapid advances in bioengineering enable the use of complex proteins as therapeutic agents to treat diseases. Compared with conventional small molecule drugs, proteins have multiple advantages, including high bioactivity and specificity with low toxicity. Developing oral dosage forms with active proteins is a route to improve patient compliance and significantly reduce production costs. However, the gastrointestinal environment remains a challenge to this delivery path due to enzymatic degradation, low permeability, and weak absorption, leading to reduced delivery efficiency and poor clinical outcomes.

AREAS COVERED

This review describes the barriers to oral delivery of peptides and complex proteins, current oral delivery strategies utilized and the opportunities and challenges ahead to try and circumvent these barriers. Oral protein drugs on the market and clinical trials provide insights and approaches for advancing delivery strategies.

EXPERT OPINION

Although most current studies on oral protein delivery rely on in vitro and in vivo animal data, the safety and limitations of the approach in humans remain uncertain. The shortage of clinical data limits the development of new or alternative strategies. Therefore, designing appropriate oral delivery strategies remains a significant challenge and requires new ideas, innovative design strategies and novel model systems.

The Chemical Space of Marine Antibacterials: Diphenyl Ethers, Benzophenones, Xanthones, and Anthraquinones

The emergence of multiresistant bacteria and the shortage of antibacterials in the drug pipeline creates the need to search for novel agents. Evolution drives the optimization of the structure of marine natural products to act as antibacterial agents. Polyketides are a vast and structurally diverse family of compounds that have been isolated from different marine microorganisms. Within the different polyketides, benzophenones, diphenyl ethers, anthraquinones, and xanthones have shown promising antibacterial activity. In this work, a dataset of 246 marine polyketides has been identified. In order to characterize the chemical space occupied by these marine polyketides, molecular descriptors and fingerprints were calculated. Molecular descriptors were analyzed according to the scaffold, and principal component analysis was performed to identify the relationships among the different descriptors. Generally, the identified marine polyketides are unsaturated, water-insoluble compounds. Among the different polyketides, diphenyl ethers tend to be more lipophilic and non-polar than the remaining classes. Molecular fingerprints were used to group the polyketides according to their molecular similarity into clusters. A total of 76 clusters were obtained, with a loose threshold for the Butina clustering algorithm, highlighting the large structural diversity of the marine polyketides. The large structural diversity was also evidenced by the visualization trees map assembled using the tree map (TMAP) unsupervised machine-learning method. The available antibacterial activity data were examined in terms of bacterial strains, and the activity data were used to rank the compounds according to their antibacterial potential. This potential ranking was used to identify the most promising compounds (four compounds) which can inspire the development of new structural analogs with better potency and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.

Defining a generic column set for achiral supercritical fluid chromatography applied to pharmaceuticals or natural products

When starting a method development in supercritical fluid chromatography (SFC), the first step is usually to screen several stationary phases based on previous experience or simply based on what is available in the laboratory. However, as there are now a large number of stationary phases available for SFC, the choice of an adequate set of columns to rapidly achieve a satisfying result can be difficult. In this project, 16 columns comprising a wide diversity of stationary phases and polarities ranging from the most polar (like bare silica gel) to the least polar (like octadecylbonded-silica) were compared, based on the gradient analysis of 129 probe compounds. The set mostly comprised active pharmaceutical ingredients, natural products and a few metabolites. The columns were ranked with the help of Derringer desirability functions taking account of (i) the number of compounds eluted from the column, (ii) the elution time in a suitable time frame, (iii) the average peak width, (iv) the average peak symmetry and (v) the spreading of retention along the gradient time. The five criteria selected showed no correlation. Overall, it appeared that those columns that had a high overall score were good for several reasons, like bare silica gel, propanediol-bonded silica or pentabromobenzyloxy-bonded silica. Initially, the columns had been screened with a gradient elution starting from 5% co-solvent and ending with 50% co-solvent in CO₂. However, for some most retentive columns like amide-bonded silica, too many compounds remained non-eluted from the column. To examine this column more fairly, a second elution gradient was applied that ended with 100% co-solvent. This proved effective in restoring good overall performance through the elution of the most polar compounds.

Radiolabelling small and biomolecules for tracking and monitoring

Radiolabelling small molecules with beta-emitters has been intensively explored in the last decades and novel concepts for the introduction of radionuclides continue to be reported regularly. New catalysts that induce carbon/hydrogen activation are able to incorporate isotopes such as deuterium or tritium into small molecules. However, these established labelling approaches have limited applicability for nucleic acid-based drugs, therapeutic antibodies, or peptides, which are typical of the molecules now being investigated as novel therapeutic modalities. These target molecules are usually larger (significantly >1 kDa), mostly multiply charged, and often poorly soluble in organic solvents. However, in preclinical research they often require radiolabelling in order to track and monitor drug candidates in metabolism, biotransformation, or pharmacokinetic studies. Currently, the most established approach to introduce a tritium atom into an oligonucleotide is based on a multistep synthesis, which leads to a low specific activity with a high level of waste and high costs. The most common way of tritiating peptides is using appropriate precursors. The conjugation of a radiolabelled prosthetic compound to a functional group within a protein sequence is a commonly applied way to introduce a radionuclide or a fluorescent tag into large molecules. This review highlights the state-of-the-art in different radiolabelling approaches for oligonucleotides, peptides, and proteins, as well as a critical assessment of the impact of the label on the properties of the modified molecules. Furthermore, applications of radiolabelled antibodies in biodistribution studies of immune complexes and imaging of brain targets are reported.

Biopharmaceutics considerations for direct oral anticoagulants

Vitamin K antagonists (VKA) and direct oral anticoagulants (DOACs) have been clinically used in the treatment of coagulation disorders. There are four DOACs approved since 2010 (dabigatran etexilate, rivaroxaban, apixaban, and edoxaban), and they were designed to overcome the practical limitations of VKA. This review summarized biopharmaceutics considerations about DOACs, which are critically discussed, applying risk analyses to subside the further classification of these drugs according to the Biopharmaceutics Classification System (BCS). These discussions included data compiled about physicochemical properties, equilibrium solubility, permeability, and drug dissolution of DOACs. From the biopharmaceutics characteristics is possible to identify critical variables related to the absorption process, which can help in the design of new formulations. The data were compared with the criteria recommended by regulatory agencies for the biopharmaceutics classification according to the BCS. From that, these data may be used to discuss the approval of generic medicines by the BCS-based biowaiver, and the clinical risks arising from novel formulations with DOACs. However, although there are indications of biopharmaceutics classifications for DOACs, conclusive information to classify these compounds according to the BCS is lacking, requiring more experimental studies to achieve this aim. Conclusive information is essential for a safe decision about the biowaiver, as well as to guide the development of new formulations containing the DOACs.

New therapeutic modalities in drug discovery and development: Insights & opportunities

New Therapeutic Modalities in Drug Discovery and Development: Insights & Opportunities (Editorial for the special issue of ADMET and DMPK)

Bioactive Marine Xanthones: A Review

The marine environment is an important source of specialized metabolites with valuable biological activities. Xanthones are a relevant chemical class of specialized metabolites found in this environment due to their structural variety and their biological activities. In this work, a comprehensive literature review of marine xanthones reported up to now was performed. A large number of bioactive xanthone derivatives (169) were identified, and their structures, biological activities, and natural sources were described. To characterize the chemical space occupied by marine-derived xanthones, molecular descriptors were calculated. For the analysis of the molecular descriptors, the xanthone derivatives were grouped into five structural categories (simple, prenylated, O-heterocyclic, complex, and hydroxanthones) and six biological activities (antitumor, antibacterial, antidiabetic, antifungal, antiviral, and miscellaneous). Moreover, the natural product-likeness and the drug-likeness of marine xanthones were also assessed. Marine xanthone derivatives are rewarding bioactive compounds and constitute a promising starting point for the design of other novel bioactive molecules.

Empirical Analysis Revealing Privileged Chemical Space of Cosmetic Preservatives

Most cosmetic products require preservation to prevent microbial contamination and to ensure consumer safety. Due to regulatory restrictions and rejection by consumers, preservative options have become limited and the development of novel solutions is needed. This search can be guided by knowledge about favorable chemical space for cosmetic preservatives. Therefore, we used preservatives allowed in the EU as training set and calculated various molecular properties. Empirical analysis revealed two separated areas of privileged chemical space with the net charge as distinctive property. The first area comprises the group of neutral and anionic preservatives and is characterized by low molecular size as well as limited hydrogen-bonding capacity, polarity, and flexibility. The second area includes cationic preservatives, which are rather diffusely distributed regarding molecular weight and hydrogen-bonding, however, all members share high flexibility. Both groups significantly differ from antibiotics, reflecting the specific requirement of cosmetic preservation. The molecular properties defining the privileged chemical space are easy to calculate, and thus, can provide guidance for the development of novel preservatives.

Prediction of Chameleonic Efficiency

Chameleonic properties, i. e., the capacity of a molecule to hide polarity in non-polar environments and expose it in water, help achieving sufficient permeability and solubility for drug molecules with high MW. We present models of experimental measures of polarity for a set of 24 FDA approved drugs (MW 405-1113) and one PROTAC (MW 1034). Conformational ensembles in aqueous and non-polar environments were generated using molecular dynamics. A linear regression model that predicts chromatographic apparent polarity (EPSA) with a mean unsigned error of 10 Ų was derived based on separate terms for donor, acceptor, and total molecular SASA. A good correlation (R² =0.92) with an experimental measure of hydrogen bond donor potential, Δlog P_oct-tol , was found for the mean hydrogen bond donor SASA of the conformational ensemble scaled with Abraham's A hydrogen bond acidity. Two quantitative measures of chameleonic behaviour, the chameleonic efficiency indices, are introduced. We envision that the methods presented herein will be useful to triage designed molecules and prioritize those with the best chance of achieving acceptable permeability and solubility.

Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies

Conformation-dependent 3D descriptors have been shown to provide better predictions of the physicochemical properties of macrocycles than 2D descriptors. However, the computational identification of relevant conformations for macrocycles is nontrivial. Herein, we report that the Caco-2 cell permeability difference between a pair of diastereomeric macrocycles correlated with their solvent accessible 3D polar surface area and radius of gyration. The descriptors were calculated from the macrocycles’ solution-phase conformational ensembles and independently from ensembles obtained by conformational sampling. Calculation of the two descriptors for three other stereo- and regioisomeric macrocycles also allowed the correct ranking of their cell permeability. Methods for conformational sampling may thus allow ranking of passive permeability for moderately flexible macrocycles, thereby contributing to the prioritization of macrocycles for synthesis in lead optimization.

Permeability prediction in the beyond-Rule-of 5 chemical space: Focus on cyclic hexapeptides

Cyclic peptides (CPs) are gaining more and more relevance in drug discovery. Since one of their main drawbacks is poor permeability, the discovery of new orally available CP drugs requires computational tools that predict CP permeability in very early drug discovery. In this study we used a literature dataset of 62 cyclic hexapeptides to evaluate the performances of a number of in silico tools based on different computational theory to model and rationalize PAMPA and Caco-2 permeability values. In particular, we submitted the dataset to a) online calculators, b) QSPR strategies, c) a physics-based tool, d) a mixed approach and e) a kinetic method. This latter is an emergent strategy in which a few relevant conformations retrieved from a set of molecular dynamics (MD) simulations by the Markov State Model (MSM) are used to establish the compounds permeability. Both free and commercial software were used. Results were compared with a model based on experimental physicochemical descriptors. All the computational approaches but online calculators performed quite well and show that lipophilicity and not polarity is the main determinant of the investigated event. A second major outcome of the study is that the impact of flexibility on the permeability of the considered dataset cannot be unambiguously assessed. Finally, our comparative analysis, which also included not common applied strategies, allowed a sound evaluation of the pros and cons of the applied computational approaches.

Challenges of peptide and protein drug delivery by oral route: Current strategies to improve the bioavailability

Advancement in biotechnology provided a notable expansion of peptide and protein therapeutics, used as antigens, vaccines, hormones. It has a prodigious potential to treat a broad spectrum of diseases such as cancer, metabolic disorders, bone disorders, and so forth. Protein and peptide therapeutics are administered parenterally due to their poor bioavailability and stability, restricting their use. Hence, research focuses on the oral delivery of peptides and proteins for the ease of self-administration. In the present review, we first address the main obstacles in the oral delivery system in addition to approaches used to enhance the stability and bioavailability of peptide/protein. We describe the physiochemical parameters of the peptides and proteins influencing bioavailability in the systemic circulation. It encounters, many barriers affecting its stability, such as poor cellular membrane permeability at the GIT site, enzymatic degradation (various proteases), and first-pass hepatic metabolism. Then describe the current approaches to overcome the challenges mentioned above by the use of absorption enhancers or carriers, structural modification, formulation and advance technology.

Pleiotropic Properties of Amphiphilic Dihydropyridines, Dihydropyridones, and Aminovinylcarbonyl Compounds

Three groups of synthetic lipids are chosen for studies: (1) 1,4-dihydropyridines (1,4-DHPs) containing two cationic moieties and their analogues; (2) 3,4-dihydro-2(1H)-pyridones containing a cationic moiety; and (3) acyclic, open-chain analogues, i.e., 2-amino-3-alkoxycarbonylalkylammonium derivatives. 1,4-DHPs possessing dodecyl alkyl chains in the ester groups in positions 3 and 5 and cationic nitrogen-containing groups in positions 2 and 6 have high cytotoxicity in cancer cells HT-1080 (human lung fibrosarcoma) and MH-22A (mouse hepatoma), but low cytotoxicity in the noncancerous NIH3T3 cells (mouse embryonic fibroblast). On the contrary, similar compounds having short (methyl, ethyl, or propoxyethyl) chains in the ester groups in positions 3 and 5 lack cytotoxicity in the cancer cells HT-1080 and MH-22A even at high doses. Inclusion of fluorine atoms in the alkyl chains in positions 3 and 5 of the DHP cycle decreases the cytotoxicity of the mentioned compounds. Structurally related dihydropyridones with a polar head group are substantially more toxic to normal and cancerous cells than the DHP analogues. Open-chain analogues of DHP lipids comprise the same conjugated aminovinylcarbonyl moiety and possess anticancer activity, but they also have high basal cytotoxicity. Electrochemical oxidation data demonstrate that oxidation potentials of selected compounds are in the range of 1.6-1.7 V for cationic 1,4-DHP, 2.0-2.4 V for cationic 3,4-dihydropyridones, and 1.2-1.5 V for 2-amino-3-alkoxycarbonylalkylammonium derivatives. Furthermore, the tested cationic 1,4-DHP amphiphiles possess antiradical activity. Molecular topological polar surface area values for the tested compounds were defined in accordance with the main fragments of compound structures. The determined logP values were highest for dodecyl ester groups in positions 3 and 5 of the 1,4-DHP and lowest for short alkyl chain-containing amphiphiles.

Chromatographic analysis of biomolecules with pressurized carbon dioxide mobile phases - A review

Biomolecules like proteins, peptides and nucleic acids widely emerge in pharmaceutical applications, either as synthetic active pharmaceutical ingredients, or from natural products as in traditional Chinese medicine. Liquid-phase chromatographic methods (LC) are widely employed for the analysis and/or purification of such molecules. On another hand, to answer the ever-increasing requests from scientists involved in biomolecules projects, other chromatographic methods emerge as useful complements to LC. In particular, there is a growing interest for chromatography with a mobile phase comprising pressurized carbon dioxide, which can be named either (i) supercritical (or subcritical) fluid chromatography (SFC) when CO₂ is the major constituent of the mobile phase, or (ii) enhanced fluidity liquid chromatography (EFLC) when hydro-organic or purely organic solvents are the major constituents of the mobile phase. Despite the low polarity of CO₂, supposedly inadequate to solubilize such biomolecules, SFC and EFLC were both employed in many occasions for this purpose. This paper specifically reviews the literature related to the SFC/EFLC analysis of free amino acids, peptides, proteins, nucleobases, nucleosides and nucleotides. The analytical conditions employed for specific molecular families are presented, with a focus on the nature of the stationary phase and the mobile phase composition. We also discuss the potential benefits of combining SFC/EFLC to LC in a single gradient elution, a method sometimes designated as unified chromatography (UC). Finally, detection issues are presented, and more particularly hyphenation to mass spectrometry.

Utility of Physicochemical Properties for the Prediction of Toxicological Outcomes: Takeda Perspective

The role that physicochemical properties play toward increasing the likelihood of toxicity findings in in vivo studies has been well reported, albeit sometimes with different conclusions. We decided to understand the role that physicochemical properties play toward the prediction of in vivo toxicological outcomes for Takeda chemistry using 284 internal compounds. In support of the previously reported "3/75 rule", reducing lipophilicity of molecules decreases toxicity odds noticeably; however, we also found that the trend of toxicity odds is different between compounds classified by their ionization state. For basic molecules, the odds of in vivo toxicity outcomes were significantly impacted by both lipophilicity and polar surface area, whereas neutral molecules were impacted less so. Through an analysis of several project-related compounds, we herein demonstrate that the utilization of the 3/75 rule coupled with consideration of ionization state is a rational strategy for medicinal chemistry design of safer drugs.

Xanthones, A Promising Anti-Inflammatory Scaffold: Structure, Activity, and Drug Likeness Analysis

Inflammation is the body's self-protective response to multiple stimulus, from external harmful substances to internal danger signals released after trauma or cell dysfunction. Many diseases are considered to be related to inflammation, such as cancer, metabolic disorders, aging, and neurodegenerative diseases. Current therapeutic approaches include mainly non-steroidal anti-inflammatory drugs and glucocorticoids, which are generally of limited effectiveness and severe side-effects. Thus, it is urgent to develop novel effective anti-inflammatory therapeutic agents. Xanthones, a unique scaffold with a 9H-Xanthen-9-one core structure, widely exist in natural sources. Till now, over 250 xanthones were isolated and identified in plants from the families Gentianaceae and Hypericaceae. Many xanthones have been disclosed with anti-inflammatory properties on different models, either in vitro or in vivo. Herein, we provide a comprehensive and up-to-date review of xanthones with anti-inflammatory properties, and analyzed their drug likeness, which might be potential therapeutic agents to fight against inflammation-related diseases.

Flexibility in early drug discovery: focus on the beyond-Rule-of-5 chemical space

Large and flexible compounds are of interest in pharmaceutical programs aimed at challenging protein targets that cannot be modulated by Rule of Five (Ro5)-compliant small molecules. Given their particular structural features, early drug discovery is now in charge of identifying which molecular descriptors should be used in the often called beyond-Rule-of-5 (bRo5) chemical space. Here, we focus on flexibility descriptors. First, we discuss the concept of flexibility and then focus on the number of rotatable bonds (NRot), the most common in silico descriptor. After identifying the pros and cons of NRot, we discuss how Kier's index Φ can replace NRot, and the limits of 3D descriptors. Finally, we show how a misuse of NRot and Φ can result in incorrect interpretations of the impact of flexibility in the bRo5 space and how flexibility has potential in the prospective design of orally bioavailable bRo5 drug candidates.

in silico screening and molecular dynamics simulations study to identify novel potent inhibitors against Mycobacterium tuberculosis DnaG primase

Tuberculosis remains a major global health threat killing millions of people. Due to existing multiple drug resistance (MDR) and prolonged treatment it becomes necessary to explore novel drug targets in Mycobacterium tuberculosis (Mtb). DnaG primase, having a significant role in primer synthesis during initiation of DNA replication, has emerged as a promising drug target. The three dimensional (3D) model of its catalytic domain (Toprim) was constructed. Further, in silico screening of the three diverse chemical compound libraries against the modeled domain was carried out. Four top screened compounds were identified and evaluated by ADMET analysis. The stability of these compounds in complex with the Toprim domain was validated through 50 ns molecular dynamics simulations. Lys 101, Glu 137 and Asp 188 in the active site predominantly formed the hydrogen bonds with the top screened compounds. Hence, the drug-like compounds identified can be taken up for the further experimental investigation as anti-tubercular agents.

Alkaloids Purified from Aristotelia chilensis Inhibit the Human α3β4 Nicotinic Acetylcholine Receptor with Higher Potencies Compared with the Human α4β2 and α7 Subtypes

The alkaloids aristoteline (1), aristoquinoline (2), and aristone (3) were purified from the leaves of the Maqui tree Aristotelia chilensis and chemically characterized by NMR spectroscopy. The pharmacological activity of these natural compounds was evaluated on human (h) α3β4, α4β2, and α7 nicotinic acetylcholine receptors (AChRs) by Ca²⁺ influx measurements. The results suggest that these alkaloids do not have agonistic, but inhibitory, activity on each receptor subtype. The obtained IC₅₀ values indicate the following receptor selectivity: hα3β4 > hα4β2 ≫ hα7. In the particular case of hα3β4 AChRs, 1 (0.40 ± 0.20 μM) and 2 (0.96 ± 0.38 μM) show higher potencies compared with 3 (167 ± 3 μM). Molecular docking and structure-activity relationship results indicate that ligand lipophilicity is important for the interaction with the luminal site located close to the cytoplasmic side of the hα3β4 ion channel between positions -2' and -4'. Compound 1 could be used as a molecular scaffold for the development of more potent noncompetitive inhibitors with higher selectivity for the hα3β4 AChR that could serve for novel addiction and depression therapies.

An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies

Histone deacetylase 8 (HDAC8) has emerged as an important therapeutic target due to its involvement in various cancerous and neurodegenerative disease states. Since pan HDAC inhibition has been linked to various side effects, the need of the hour is to develop inhibitors truly selective for one isoform. This work attempts to explore the structural basis of selective HDAC8 inhibition by docking, pharmacophore and 3 D QSAR studies of 53 highly potent and highly selective triazol-based hydroxamic acid inhibitors. The binding modes of these novel inhibitors have been explored via Glide XP (Extra Precision) and induced-fit docking (IFD) strategies. The IFD poses of highly active and selective inhibitors showed conformational changes in active site residues like Trp141, Phe152 and Phe208, which were further verified by molecular dynamics simulations. A new CH-π interaction, which is atypical of HDAC inhibitors, was also observed in case of some highly selective inhibitors. Two pharmacophore models have been proposed; one highlights the structural basis of potency of these inhibitors and the other focuses on the selectivity. The corresponding QSAR models, obtained from alignment of the inhibitors as per the proposed pharmacophore models, are highly statistically significant. These models highlight the importance of size of the hydrophobic and aromatic groups present in the inhibitors and their contribution to activity of the inhibitors. The ADMET properties of the ligand library have also been analyzed and the predicted descriptors have been correlated with activity using principal components analysis to gain insight into the effect of pharmacokinetic properties on the activity.Communicated by Ramaswamy H. Sarma.

Structures, Activities and Drug-Likeness of Anti-Infective Xanthone Derivatives Isolated from the Marine Environment: A Review

Marine organisms represent almost half of total biodiversity and are a very important source of new bioactive substances. Within the varied biological activities found in marine products, their antimicrobial activity is one of the most relevant. Infectious diseases are responsible for high levels of morbidity and mortality and many antimicrobials lose their effectiveness with time due to the development of resistance. These facts justify the high importance of finding new, effective and safe anti-infective agents. Among the variety of biological activities of marine xanthone derivatives, one that must be highlighted is their anti-infective properties. In this work, a literature review of marine xanthones with anti-infective activity, namely antibacterial, antifungal, antiparasitic and antiviral, is presented. Their structures, biological activity, sources and the methods used for bioactivity evaluation are described. The xanthone derivatives are grouped in three sets: xanthones, hydroxanthones and glycosylated derivatives. Moreover, molecular descriptors, biophysico-chemical properties, and pharmacokinetic parameters were calculated, and the chemical space occupied by marine xanthone derivatives is recognized. The chemical space was compared with marketed drugs and framed accordingly to the drug-likeness concept in order to profile the pharmacokinetic of anti-infective marine xanthone derivatives.

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Conformational flexibility is a major determinant of the properties of macrocycles and other drugs in beyond rule of 5 (bRo5) space. Prediction of conformations is essential for design of drugs in this space, and we have evaluated three tools for conformational sampling of a set of 10 bRo5 drugs and clinical candidates in polar and apolar environments. The distance-geometry based OMEGA was found to yield ensembles spanning larger structure and property spaces than the ensembles obtained by MOE-LowModeMD (MOE) and MacroModel (MC). Both MC and OMEGA but not MOE generated different ensembles for polar and apolar environments. All three conformational search methods generated conformers similar to the crystal structure conformers for 9 of the 10 compounds, with OMEGA performing somewhat better than MOE and MC. MOE and OMEGA found all six conformers of roxithromycin that were identified by NMR in aqueous solutions, whereas only OMEGA sampled the three conformers observed in chloroform. We suggest that characterization of conformers using molecular descriptors, e.g., the radius of gyration and polar surface area, is preferred to energy- or root-mean-square deviation-based methods for selection of biologically relevant conformers in drug discovery in bRo5 space.

Repeatability of n-octanol/water partition coefficient values between liquid chromatography measurement methods

The n-octanol/water partition coefficient (K_OW) is a physical/chemical property that is extensively used for regulatory and environmental risk and exposure assessments. The K_OW value can estimate various chemical properties such as water solubility, bioavailability, and toxicity using quantitative structure-activity relationships which demands an accurate knowledge of this property. The present investigation aims to compare outcomes of three commonly cited methods of K_OW measurement in the literature for six hydrophobic chemicals with insecticidal functions as well as highly volatile petroleum constituents. This measurement has been difficult to obtain for the selected pyrethroid insecticides, cypermethrin, and bifenthrin and is a novel measurement for the latter: polycyclic aromatic sulfur heterocycles, dibenzothiophene (DBT), and three of its alkyl derivatives except for DBT. The K_OW values were obtained using two liquid chromatographic methods with isocratic and gradient programming, and the slow-stirring method following OECD 117 and 123 guidelines, respectively. The mean log K_OW values of bifenthrin, cypermethrin, DBT, methyl-DBT, dimethyl-DBT, and diethyl-DBT were 8.4 ± 0.1, 6.0 ± 0.3, 4.8 ± 0.0, 5.4 ± 0.1, 6.0 ± 0.1, and 6.8 ± 0.0 using the HPLC method with gradient programing. The K_OW values were significantly reproducible within a method, however, not between the methods. Results suggest assessing a chemical's property and environmental risk and exposure solely based on the K_OW value should be practiced with caution.

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Conformational flexibility has been proposed to significantly affect drug properties outside rule-of-5 (Ro5) chemical space. Here, we investigated the influence of dynamically exposed polarity on cell permeability and aqueous solubility for a structurally diverse set of drugs and clinical candidates far beyond the Ro5, all of which populated multiple distinct conformations as revealed by X-ray crystallography. Efflux-inhibited (passive) Caco-2 cell permeability correlated strongly with the compounds' minimum solvent-accessible 3D polar surface areas (PSA), whereas aqueous solubility depended less on the specific 3D conformation. Inspection of the crystal structures highlighted flexibly linked aromatic side chains and dynamically forming intramolecular hydrogen bonds as particularly effective in providing "chameleonic" properties that allow compounds to display both high cell permeability and aqueous solubility. These structural features, in combination with permeability predictions based on the correlation to solvent-accessible 3D PSA, should inspire drug design in the challenging chemical space far beyond the Ro5.

Learning how to use IAM chromatography for predicting permeability

The interest for IAM (Immobilized Artificial Membranes) chromatography in the prediction of drug permeability is increasing. Here we firstly set-up a dataset of 253 molecules including neutral and ionized drugs and few organic compounds for which we either measured or retrieved from the literature IAM.PC.DD2 log K_w^IAM data. Then we applied block relevance (BR) analysis to extract from PLS models the relative contribution of intermolecular forces governing log K_w^IAM and Δlog K_w^IAM (a combined descriptor calculated from log K_w^IAM). Finally, the relationship between log K_w^IAM, Δlog K_w^IAM and passive permeability determined in both PAMPA and MDCK-LE systems was looked for. Models provided the basis for a rational application of IAM chromatography in permeability prediction.

Triterpenoids from Ganoderma lucidum inhibit the activation of EBV antigens as telomerase inhibitors

Nasopharyngeal carcinoma (NPC) is a malignant disease that threatens the health of humans. To find effective agents for the inhibition of Epstein-Barr virus (EBV) infection, which is associated with NPC, a phytochemical investigation of Ganoderma lucidum was carried out in the present study. Five triterpenoids were identified, including ganoderic acid A (compound 1), ganoderic acid B (compound 2), ganoderol B (compound 3), ganodermanontriol (compound 4), and ganodermanondiol (compound 5), on the basis of spectroscopic analysis. An inhibition of EBV antigens activation assay was implemented to elucidate the triterpenoids from G. lucidum and potentially prevent NPC. All the triterpenoids showed significant inhibitory effects on both EBV EA and CA activation at 16 nmol. At 3.2 nmol, all the compounds moderately inhibited the activation of the two antigens. The activity of telomerase was inhibited by these triterpenoids at 10 µM. Molecular docking demonstrated that compound 1 was able to inhibit telomerase as a ligand. In addition, the physicochemical properties of these compounds were calculated to elucidate their drug-like properties. These results provided evidence for the application of these triterpenoids and whole G. lucidum in the treatment of NPC.

High throughput methods to measure the propensity of compounds to form intramolecular hydrogen bonding

Implementation of IMHB considerations in drug discovery needs robust and validated descriptors to experimentally verify the propensity of compounds to exhibit IMHBs. The first part of the paper presents an overview of the most common techniques to measure the propensity of compounds to form IMHBs. Then we review and discuss recently proposed high throughput (HT) physicochemical descriptors (i.e. Δlog Poct-tol, EPSA and log k'80 PLRP-S) which provide the same information. Analysis of the available data enabled us to extract guidelines for the application of these descriptors in drug discovery programs.