Chemical Structure-Related Drug-Like Criteria of Global Approved Drugs

Discovery of Novel Antiosteoporosis Leads with Bone Resorption Inhibition and Anabolic Promotion through a Chemotype-Assembly Approach

Developing a dual-efficiency agent with antiresorptive and anabolic applications is a promising strategy for treating osteoporosis. This study reports the discovery of dual antiosteoporosis agents via a chemotype-assembly approach. Chemotype analysis identified 12 antiresorptive and 12 anabolic chemotypes and 7 dual-function chemotype-assembly rules. Based on these assembly rules, a dual-functional compound S24 was discovered. S24 exhibits osteoclastogenesis inhibition with an IC50 value of 10.28 μM and osteoblast differentiation stimulation at 10 μM. S24 derivatives were designed and synthesized based on the activity relationship of the chemotypes. This yielded a more active compound, S24-14, with an osteoclastogenesis inhibition IC50 value of 0.40 μM and osteoblast differentiation stimulation at 1.0 μM; compound S24-14 also suppressed bone loss in vivo. These results prove that S24-14 can be a potential lead for antiosteoporosis drug development.

Integrated ML-Based Strategy Identifies Drug Repurposing for Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) affects an estimated global population of around 3 million individuals. IPF is a medical condition with an unknown cause characterized by the formation of scar tissue in the lungs, leading to progressive respiratory disease. Currently, there are only two FDA-approved small molecule drugs specifically for the treatment of IPF and this has created a demand for the rapid development of drugs for IPF treatment. Moreover, denovo drug development is time and cost-intensive with less than a 10% success rate. Drug repurposing currently is the most feasible option for rapidly making the drugs to market for a rare and sporadic disease. Normally, the repurposing of drugs begins with a screening of FDA-approved drugs using computational tools, which results in a low hit rate. Here, an integrated machine learning-based drug repurposing strategy is developed to significantly reduce the false positive outcomes by introducing the predock machine-learning-based predictions followed by literature and GSEA-assisted validation and drug pathway prediction. The developed strategy is deployed to 1480 FDA-approved drugs and to drugs currently in a clinical trial for IPF to screen them against "TGFB1", "TGFB2", "PDGFR-a", "SMAD-2/3", "FGF-2", and more proteins resulting in 247 total and 27 potentially repurposable drugs. The literature and GSEA validation suggested that 72 of 247 (29.14%) drugs have been tried for IPF, 13 of 247 (5.2%) drugs have already been used for lung fibrosis, and 20 of 247 (8%) drugs have been tested for other fibrotic conditions such as cystic fibrosis and renal fibrosis. Pathway prediction of the remaining 142 drugs was carried out resulting in 118 distinct pathways. Furthermore, the analysis revealed that 29 of 118 pathways were directly or indirectly involved in IPF and 11 of 29 pathways were directly involved. Moreover, 15 potential drug combinations are suggested for showing a strong synergistic effect in IPF. The drug repurposing strategy reported here will be useful for rapidly developing drugs for treating IPF and other related conditions.

Ruthenium(II)-Catalyzed Late-Stage Incorporation of N-Aryl Triazoles and Tetrazoles with Sulfonium Salts via C-H Activation

The late-stage functionalization of active pharmaceutical ingredients is a key challenge in medicinal chemistry. Furthermore, N-aryl triazoles and tetrazoles are important structural motifs with the potential to boost the activity of diverse drug molecules. Using easily accessible dibenzothiophenium salts for the ruthenium-catalyzed C-H arylation, these scaffolds were introduced into a variety of bioactive compounds. Our methodology uses cost-efficient ruthenium, KOAc as a mild base and gives access to a plethora of highly decorated triazole and tetrazole containing drug derivatives.

Research progress of prodrugs for the treatment of cerebral ischemia

It is well-known that pharmacotherapy plays a pivotal role in the treatment and prevention of cerebral ischemia. Nevertheless, existing drugs, including numerous natural products, encounter various challenges when applied in cerebral ischemia treatment. These challenges comprise poor brain absorption due to low blood-brain barrier (BBB) permeability, limited water solubility, inadequate bioavailability, poor stability, and rapid metabolism. To address these issues, researchers have turned to prodrug strategies, aiming to mitigate or eliminate the adverse properties of parent drug molecules. In vivo metabolism or enzymatic reactions convert prodrugs into active parent drugs, thereby augmenting BBB permeability, improving bioavailability and stability, and reducing toxicity to normal tissues, ultimately aiming to enhance treatment efficacy and safety. This comprehensive review delves into multiple effective prodrug strategies, providing a detailed description of representative prodrugs developed over the past two decades. It underscores the potential of prodrug approaches to improve the therapeutic outcomes of currently available drugs for cerebral ischemia. The publication of this review serves to enrich current research progress on prodrug strategies for the treatment and prevention of cerebral ischemia. Furthermore, it seeks to offer valuable insights for pharmaceutical chemists in this field, offer guidance for the development of drugs for cerebral ischemia, and provide patients with safer and more effective drug treatment options.

AIGO-DTI: Predicting Drug-Target Interactions Based on Improved Drug Properties Combined with Adaptive Iterative Algorithms

Artificial intelligence-based methods for predicting drug-target interactions (DTIs) aim to explore reliable drug candidate targets rapidly and cost-effectively to accelerate the drug development process. However, current methods are often limited by the topological regularities of drug molecules, making them difficult to generalize to a broader chemical space. Additionally, the use of similarity to measure DTI network links often introduces noise, leading to false DTI relationships and affecting the prediction accuracy. To address these issues, this study proposes an Adaptive Iterative Graph Optimization (AIGO)-DTI prediction framework. This framework integrates atomic cluster information and enhances molecular features through the design of functional group prompts and graph encoders, optimizing the construction of DTI association networks. Furthermore, the optimization of graph structure is transformed into a node similarity learning problem, utilizing multihead similarity metric functions to iteratively update the network structure to improve the quality of DTI information. Experimental results demonstrate the outstanding performance of AIGO-DTI on multiple public data sets and label reversal data sets. Case studies, molecular docking, and existing research validate its effectiveness and reliability. Overall, the method proposed in this study can construct comprehensive and reliable DTI association network information, providing new graphing and optimization strategies for DTI prediction, which contribute to efficient drug development and reduce target discovery costs.

Recent developments in the enzymatic modifications of steroid scaffolds

Steroids are an important family of bioactive compounds. Steroid drugs are renowned for their multifaceted pharmacological activities and are the second-largest category in the global pharmaceutical market. Recent developments in biocatalysis and biosynthesis have led to the increased use of enzymes to enhance the selectivity, efficiency, and sustainability for diverse modifications of steroids. This review discusses the advancements achieved over the past five years in the enzymatic modifications of steroid scaffolds, focusing on enzymatic hydroxylation, reduction, dehydrogenation, cascade reactions, and other modifications for future research on the synthesis of novel steroid compounds and related drugs, and new therapeutic possibilities.

Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants

Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.

NHC-Catalyzed Formal [4 + 2] Annulation of o-Formyl-Tethered Michael Acceptors and Ynones to Access Highly Functionalized Naphthalene Derivatives

Herein we demonstrate a novel organocatalytic method to access multifunctionalized naphthalenes via an NHC-catalyzed reaction of ynones and o-formyl-tethered Michael acceptors. The presented method proceeds through an intermolecular Stetter reaction-cyclization-aromatization cascade and represents a rare example of organocatalytic benzannulation for the synthesis of substituted arenes by using ynone as a two-carbon synthon. The current method has broad substrate scope; postsynthetic transformations and gram-scale syntheses highlight the practicality of the displayed methodology.

Medicinal-Chemistry-Driven Approach to 2-Substituted Benzoxazole-Estradiol Chimeras: Synthesis, Anticancer Activity, and Early ADME Profile

The efficient synthesis of novel estradiol-based A-ring-fused oxazole derivatives, which can be considered as benzoxazole-steroid domain-integrated hybrids containing a common benzene structural motif, is described. The target compounds were prepared from steroidal 2-aminophenol precursors by heterocycle formation or functional group interconversion (FGI) strategies. According to 2D projection-based t-distributed stochastic neighbor embedding (t-SNE), the novel molecules were proved to represent a new chemical space among steroid drugs. They were characterized based on critical physicochemical parameters using in silico and experimental data. The performance of the compounds to inhibit cell proliferation was tested on four human cancer cell lines and non-cancerous cells. Further examinations were performed to reveal IC50 and lipophilic ligand efficiency (LLE) values, cancer cell selectivity, and apoptosis-triggering features. Pharmacological tests and LLE metric revealed that some derivatives, especially the 2-(4-ethylpiperazin-1-yl)oxazole derivative exhibit strong anticancer activity and trigger the apoptosis of cancer cells with relatively low promiscuity risk similarly to the structurally most closely-related and intensively studied anticancer agent, 2-methoxy-estradiol.

Molecular modelling of SdiA protein by selected flavonoid and terpenes compounds to attenuate virulence in Klebsiella pneumoniae

Klebsiella pneumoniae is one of the perturbing multidrug resistant (MDR) and ESKAPE pathogens contributing to the mounting morbidity, mortality and extended rate of hospitalization. Its virulence, often regulated by quorum sensing (QS) reinforces the need to explore alternative and prospective antivirulence agents, relatively from plants secondary metabolites. Computer aided drug discovery using molecular modelling techniques offers advantage to investigate prospective drugs to combat MDR pathogens. Thus, this study employed virtual screening of selected terpenes and flavonoids from medicinal plants to interrupt the QS associated SdiA protein in K. pneumoniae to attenuate its virulence. 4LFU was used as a template to model the structure of SdiA. ProCheck, Verify3D, Ramachandran plot scores, and ProSA-Web all attested to the model's good quality. Since SdiA protein in K. pneumoniae leads to the expression of virulence, 31 prospective bioactive compounds were docked for antagonistic potential. The stability of the protein-ligand complex, atomic motions and inter-atomic interactions were further investigated through molecular dynamics simulations (MDS) at 100 ns production runs. The binding free energy was estimated using the molecular mechanics/poisson-boltzmann surface area (MM/PB-SA). Furthermore, the drug-likeness properties of the studied compounds were validated. Docking studies showed phytol possesses the highest binding affinity (-9.205 kcal/mol) while glycitein had -9.752 kcal/mol highest docking score. The MDS of the protein in complex with the best-docked compounds revealed phytol with the highest binding energy of -44.2625 kcal/mol, a low root-mean-square deviation (RMSD) value of 1.54 Å and root-mean-square fluctuation (RMSF) score of 1.78 Å. Analysis of the drug-likeness properties prediction and bioavailability of these compounds revealed their conformed activity to lipinski's rules with bioavailability scores of 0.55 F. The studied terpenes and flavonoids compounds effectively thwart SdiA protein, therefore regulate inter- or intra cellular communication and associated in virulence Enterobacteriaceae, serving as prospective antivirulence drugs.Communicated by Ramaswamy H. Sarma.

Research in the Field of Drug Design and Development

The processes used by academic and industrial scientists to discover new drugs have recently experienced a true renaissance, with many new and exciting techniques being developed over the past 5-10 years alone. Drug design and discovery, and the search for new safe and well-tolerated compounds, as well as the ineffectiveness of existing therapies, and society's insufficient knowledge concerning the prophylactics and pharmacotherapy of the most common diseases today, comprise a serious challenge. This can influence not only the quality of human life, but also the health of whole societies, which became evident during the COVID-19 pandemic. In general, the process of drug development consists of three main stages: drug discovery, preclinical development using cell-based and animal models/tests, clinical trials on humans and, finally, forward moving toward the step of obtaining regulatory approval, in order to market the potential drug. In this review, we will attempt to outline the first three most important consecutive phases in drug design and development, based on the experience of three cooperating and complementary academic centers of the Visegrád group; i.e., Medical University of Lublin, Poland, Masaryk University of Brno, Czech Republic, and Comenius University Bratislava, Slovak Republic.

Antiproliferative, molecular docking, and bioavailability studies of diarylheptanoids isolated from stem bark of Garuga pinnata Rox B

Diarylheptanoids are a major class of plant secondary metabolites characterized by 1, 7-diphenyl heptanes in a seven-member carbon frame. In the present study, diarylheptanoids (garuganins 1, 3, 4 and 5) isolated from Garuga pinnata stem bark were evaluated for cytotoxic activity against MCF-7 and HCT15 cancer cell lines. Among the tested compounds, garuganin 5 and 3 exhibited the highest cytotoxic activity against HCT15 and MCF-7 with IC50 2.9 ± 00.8 μg/mL, 3.3 ± 0.1 μg/mL and 3.2 ± 0.1 μg/mL, and 3.5 ± 0.3 μg/mL, respectively. The molecular docking of garuganin 1, 3, 4 and 5 exhibited significant affinity toward the tested EGFR 4Hjo protein. The free energy and inhibitory constant of the compounds ranged from - 7.47 to - 8.49 kcal/mol and 3.34 micromolar to 944.20 nM nanomolar, respectively. Based on the results of cytotoxic activity, garuganin 5 and 3 were further evaluated for time- and concentration-dependent intracellular accumulation studies. The time-dependent intracellular concentration of garuganin 3 and 5 after 5 h of incubation increased about 5.5- and 4.5-fold, 204.16 ± 0.02 and 145.4 ± 0.36 nmol/L mg, respectively. The concentration-dependent intracellular concentration of garuganin 3 and 5 at 200 µg/mL increased of about > 12- and ninefold, 186.22 ± 0.05 and 98.73 ± 0.02 nmol/L mg, respectively. The intracellular concentrations of garuganin 3 and 5, in the presence of verapamil, cyclosporine and MK 571, was found to be significant in the basal direction compared to the apical directions. The results indicate that, garuganin 3 and 5 exhibited significant cytotoxic activity against MCF-7 and HCT15 cancer cell lines and also exhibited high binding affinity toward EGFR protein compared to garuganin 1 and 4.

Antibiofilm and Anti-Quorum-Sensing Activities of Novel Pyrazole and Pyrazolo[1,5-a]pyrimidine Derivatives as Carbonic Anhydrase I and II Inhibitors: Design, Synthesis, Radiosterilization, and Molecular Docking Studies

Nowadays, searching for new anti-infective agents with diverse mechanisms of action has become necessary. In this study, 16 pyrazole and pyrazolo[1,5-a]pyrimidine derivatives were synthesized and assessed for their preliminary antibacterial and antibiofilm activities. All these derivatives were initially screened for their antibacterial activity against six clinically isolated multidrug resistance by agar well-diffusion and broth microdilution methods. The initial screening presented significant antibacterial activity with a bactericidal effect for five compounds, namely 3a, 5a, 6, 9a, and 10a, compared with Erythromycin and Amikacin. These five derivatives were further evaluated for their antibiofilm activity against both S. aureus and P. aeruginosa, which showed strong biofilm-forming activity at their MICs by >60%. The SEM analysis confirmed the biofilm disruption in the presence of these derivatives. Furthermore, anti-QS activity was observed for the five hybrids at their sub-MICs, as indicated by the visible halo zone. In addition, the presence of the most active derivatives reduces the violacein production by CV026, confirming that these compounds yielded anti-QS activity. Furthermore, these compounds showed strong inhibitory action against human carbonic anhydrase (hCA-I and hCA-II) isoforms with IC50 values ranging between 92.34 and 168.84 nM and between 73.2 and 161.22 nM, respectively. Finally, radiosterilization, ADMET, and a docking simulation were performed.

Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using a Docking Approach

A de novo assembly algorithm is provided to propose the assembly of bitopic transmembrane domains (TMDs) of membrane proteins. The algorithm is probed using, in particular, viral channel forming proteins (VCPs) such as M2 of influenza A virus, E protein of severe acute respiratory syndrome corona virus (SARS-CoV), 6K of Chikungunya virus (CHIKV), SH of human respiratory syncytial virus (hRSV), and Vpu of human immunodeficiency virus type 2 (HIV-2). The generation of the structures is based on screening a 7-dimensional space. Assembly of the TMDs can be achieved either by simultaneously docking the individual TMDs or via a sequential docking. Scoring based on estimated binding energies (EBEs) of the oligomeric structures is obtained by the tilt to decipher the handedness of the bundles. The bundles match especially well for all-atom models of M2 referring to an experimentally reported tetrameric bundle. Docking of helical poly-peptides to experimental structures of M2 and E protein identifies improving EBEs for positively charged (K,R,H) and aromatic amino acids (F,Y,W). Data are improved when using polypeptides for which the coordinates of the amino acids are adapted to the Cα coordinates of the respective experimentally derived structures of the TMDs of the target proteins.

Newly Synthesized Melphalan Analogs Induce DNA Damage and Mitotic Catastrophe in Hematological Malignant Cancer Cells

Myeloablative therapy with highdoses of the cytostatic drug melphalan (MEL) in preparation for hematopoietic cell transplantation is the standard of care for multiple myeloma (MM) patients. Melphalan is a bifunctional alkylating agent that covalently binds to nucleophilic sites in the DNA and effective in the treatment, but unfortunately has limited therapeutic benefit. Therefore, new approaches are urgently needed for patients who are resistant to existing standard treatment with MEL. Regulating the pharmacological activity of drug molecules by modifying their structure is one method for improving their effectiveness. The purpose of this work was to analyze the physicochemical and biological properties of newly synthesized melphalan derivatives (EE-MEL, EM-MEL, EM-MOR-MEL, EM-I-MEL, EM-T-MEL) obtained through the esterification of the carboxyl group and the replacement of the the amino group with an amidine group. Compounds were selected based on our previous studies for their improved anticancer properties in comparison with the original drug. For this, we first evaluated the physicochemical properties using the circular dichroism technique, then analyzed the zeta potential and the hydrodynamic diameters of the particles. Then, the in vitro biological properties of the analogs were tested on multiple myeloma (RPMI8226), acute monocytic leukemia (THP1), and promyelocytic leukemia (HL60) cells as model systems for hematological malignant cells. DNA damage was assessed by immunostaining γH2AX, cell cycle distribution changes by propidium iodide (PI) staining, and cell death by the activation of caspase 2. We proved that the newly synthesized derivatives, in particular EM-MOR-MEL and EM-T-MEL, affected the B-DNA conformation, thus increasing the DNA damage. As a result of the DNA changes, the cell cycle was arrested in the S and G2/M phases. The cell death occurred by activating a mitotic catastrophe. Our investigations suggest that the analogs EM-MOR-MEL and EM-T-MEL have better anti-cancer activity in multiple myeloma cells than the currently used melphalan.

Substitutional Diversity-Oriented Synthesis and In Vitro Anticancer Activity of Framework-Integrated Estradiol-Benzisoxazole Chimeras

Hybridization of steroids and other pharmacophores often modifies the bioactivity of the parent compounds, improving selectivity and side effect profile. In this study, estradiol and 3′-(un)substituted benzisoxazole moieties were combined into novel molecules by structural integration of their aromatic rings. Simple estrogen starting materials, such as estrone, estradiol and estradiol-3-methylether were used for the multistep transformations. Some of the heterocyclic derivatives were prepared from the estrane precursor by a formylation or Friedel–Crafts acylation—oximation—cyclization sequence, whereas others were obtained by a functional group interconversion strategy. The antiproliferative activities of the synthesized compounds were assessed on various human cervical, breast and prostate cancer cell lines (HeLa, MCF-7, PC3, DU-145) and non-cancerous MRC-5 fibroblast cells. Based on the primary cytotoxicity screens, the most effective cancer-selective compounds were selected, their IC₅₀ values were determined and their apoptosis-inducing potential was evaluated by quantitative real-time PCR. Pharmacological studies revealed a strong structure–function relationship, where derivatives with a hydroxyl group on C-17 exhibited stronger anticancer activity compared to the 17-acetylated counterparts. The present study concludes that novel estradiol-benzisoxazole hybrids exert remarkable cancer cell-specific antiproliferative activity and trigger apoptosis in cancer cells.

Conditional reduction of the loss value versus reinforcement learning for biassing a de-novo drug design generator

Deep learning has demonstrated promising results in de novo drug design. Often, the general pipeline consists of training a generative model (G) to learn the building rules of valid molecules, then using a biassing technique such as reinforcement learning (RL) to focus G on the desired chemical space. However, this sequential training of the same model for different tasks is known to be prone to a catastrophic forgetting (CF) phenomenon. This work presents a novel yet simple approach to bias G with significantly less CF than RL. The proposed method relies on backpropagating a reduced value of the cross-entropy loss used to train G according to the proportion of desired molecules that the biased-G can generate. We named our approach CRLV, short for conditional reduction of the loss value. We compared the two biased models (RL-biased-G and CRLV-biased-G) for four different objectives related to de novo drug design.CRLV-biased-G outperformed RL-biased-G in all four objectives and manifested appreciably less CF. Besides, an intersection analysis between molecules generated by the RL-biased-G and the CRLV-biased-G revealed that they can be used jointly without losing diversity given the low percentage of overlap between the two to further increase the desirability. Finally, we show that the difficulty of an objective is proportional to (i) its frequency in the dataset used to train G and (ii) the associated structural variance (SV), which is a new parameter we introduced in this paper, calling for novel exploration techniques for such difficult objectives.

Marine Alga Ulva fasciata-Derived Molecules for the Potential Treatment of SARS-CoV-2: An In Silico Approach

SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This in silico study aimed to elucidate therapeutic efficacies against SARS-CoV-2 of phyco-compounds from the seaweed, Ulva fasciata. Twelve phyco-compounds were isolated and toxicity was analyzed by VEGA QSAR. Five compounds were found to be nonmutagenic, noncarcinogenic and nontoxic. Moreover, antiviral activity was evaluated by PASS. Binding affinities of five of these therapeutic compounds were predicted to possess probable biological activity. Fifteen SARS-CoV-2 target proteins were analyzed by the AutoDock Vina program for molecular docking binding energy analysis and the 6Y84 protein was determined to possess optimal binding affinities. The Desmond program from Schrödinger's suite was used to study high performance molecular dynamic simulation properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol-6Y84 for better drug evaluation. The ligand with 6Y84 had stronger binding affinities (-5.9 kcal/mol) over two standard drugs, Chloroquine (-5.6 kcal/mol) and Interferon α-2b (-3.8 kcal/mol). Swiss ADME calculated physicochemical/lipophilicity/water solubility/pharmacokinetic properties for 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, showing that this therapeutic agent may be effective against SARS-CoV-2.

Terminal Phenoxy Group as a Privileged Moiety of the Drug Scaffold-A Short Review of Most Recent Studies 2013-2022

The terminal phenoxy group is a moiety of many drugs in use today. Numerous literature reports indicated its crucial importance for biological activity; thus, it is a privileged scaffold in medicinal chemistry. This review focuses on the latest achievements in the field of novel potential agents bearing a terminal phenoxy group in 2013-2022. The article provided information on neurological, anticancer, potential lymphoma agent, anti-HIV, antimicrobial, antiparasitic, analgesic, anti-diabetic as well as larvicidal, cholesterol esterase inhibitors, and antithrombotic or agonistic activities towards the adrenergic receptor. Additionally, for selected agents, the Structure-Activity-Relationship (SAR) is also discussed. Thus, this study may help the readers to better understand the nature of the phenoxy group, which will translate into rational drug design and the development of a more efficient drug. To the best of our knowledge, this is the first review devoted to an in-depth analysis of the various activities of compounds bearing terminal phenoxy moiety.

Synthesis and Biological Activity Characterization of Novel 5-Oxopyrrolidine Derivatives with Promising Anticancer and Antimicrobial Activity

The 1-(4-acetamidophenyl)-5-oxopyrrolidine carboxylic acid was applied for synthesizing derivatives bearing azole, diazole, and hydrazone moieties in the molecule. Modification of an acetamide fragment to the free amino group afforded compounds with two functional groups, which enabled to provide a series of 4-substituted-1-(4-substituted phenyl)pyrrolidine-2-ones. The resulted compounds 2 and 4-22 were subjected to the in vitro anticancer and antimicrobial activity determination. The compounds 18-22 exerted the most potent anticancer activity against A549 cells. Furthermore, compound 21 bearing 5-nitrothiophene substituents demonstrated promising and selective antimicrobial activity against multidrug-resistant Staphylococcus aureus strains, including linezolid and tedizolid-resistant S. aureus. These results demonstrate that 5-oxopyrolidine derivatives are attractive scaffolds for the further development of anticancer and antimicrobial compounds targeting multidrug-resistant Gram-positive pathogens.

Quinoline, with the active site of 8-hydroxyl, efficiently inhibits Micropterus salmoides rhabdovirus (MSRV) infection in vitro and in vivo

Micropterus salmoides rhabdovirus (MSRV) is an significant pathogen that causes high mortality and related economic losses in bass aquaculture. There is no effective or approved therapy to date. In this study, we evaluated the anti-MSRV effects of 22 quinoline derivatives in grass carp ovary (GCO) cells. Among these compounds, 8-hydroxyquinoline exhibited valid inhibition in decreasing MSRV nucleoprotein gene expression levels of 99.3% with a half-maximal inhibitory concentrations (IC₅₀ ) value of 4.66 μM at 48 h. Moreover, 8-hydroxyquinoline significantly enhanced a protective effect in GCO cells by reducing the cytopathic effect (CPE). By comparing the anti-MSRV activity of 22 quinoline derivatives, we found that 8-hydroxyquinoline possessed the efficient active site of 8-hydroxyl and inhibited MSRV infection in vitro. For in vivo studies, 8-hydroxyquinoline via intraperitoneal injection exhibited an antiviral effect in MSRV-infected largemouth bass by substantially enhancing the survival rate by 15.0%. Importantly, the viral loads in the infected largemouth bass notably reduced in the spleen on the third days post-infection. Overall, 8-hydroxyquinoline was considered to be an efficient agent against MSRV in aquaculture.

Computational approaches for evaluation of isobavachin as potential inhibitor against t877a and w741l mutations in prostate cancer

Prostate cancer is the World's second most common cancer, with the fifth-highest male mortality rate. Point mutations such as T877A and W741L are frequently seen in advanced prostate cancer patients, conferring drug-resistance and hence driving cancer growth. Such occurrence of drug resistance in prostate cancer necessitates designing of suitable ligands to ensure better interactions with the receptors which can block the progression of the disease. The present study focus on the modification of plant-derived flavonoids that might act as inhibitors against such point mutations namely, T877A and W741L. In T877A mutation threonine is substituted by alanine at the 877 codon and W741L mutation, tryptophan is substituted by lysine at the 741 codon in prostate cancer. The study revolved on the aspect of the evaluation of Isobavachin and its derivatives as a potential agent to tackle such point mutations by using the in silico approach. A total of 98 molecular dockings were performed to find the ligand-receptor complexes with the lowest binding energy employing Autodock Software to conduct the blind and site-specific docking. Additionally, ligands were screened for Drug-likeness and toxicity using several tools yielding eight possible drug candidates. Based on the results of Molecular Docking, Drug-likeness, and ADMET testing, ten structures, including six complexes and three receptors were subjected to molecular dynamics simulation of 100 ns covering RMSD, RMSF, Rg, and MM/PBSA. Based on the simulation results, Isobavachin, IsoMod4, and IsoMod7 were concluded to be stable and exhibited potential properties for developing a novel drug to combat prostate cancer and its associated drug-resistance.

phytochemdb: a platform for virtual screening and computer-aided drug designing

The phytochemicals of medicinal plants are regarded as a rich source of diverse chemical spaces that have been used as supplements and alternative medicines in the millennium. Even in this era of combinatorial chemical drugs, phytomedicines account for a large share of the statistics of newly approved drugs. In the field of computational aided and rational drug design, there is an urgent need to develop and build a useful phytochemical database management system with a user-friendly interface that allows proper data storage, retrieval and management. We showed ‘phytochemdb’, a manually managed database that compiles 525 plants and their corresponding 8093 phytochemicals, aiming to incorporate the activities of phytochemicals from medicinal plants. The database collects molecular formula, three-dimensional/two-dimensional structure, canonical SMILES, molecular weight, no. of heavy atoms, no. of aromatic heavy atoms, fraction Csp3, no. of rotatable bonds, no. of H-bond acceptors, no. of H-bond donors, molar refractivity, topological polar surface area, gastrointestinal absorption, Blood–Brain Barrier (BBB) permeant, P-gp substrate, CYP1A2 inhibitor, CYP2C19 inhibitor, CYP2C9 inhibitor, CYP2D6 inhibitor, CYP3A4 inhibitor, Log Kp, Ghose, Veber, Egan, Muegge, bioavailability scores, pan-assay interference compounds, Brenk, Leadlikeness, synthetic accessibility, iLOGP and Lipinski rule of five with the number of violations for each compound. It provides open contribution functions for the researchers who screen phytochemicals in the laboratory and have released their data. ‘phytochemdb’ is a comprehensive database that gathers most of the information about medicinal plants in one platform, which is considered to be very beneficial to the work of researchers on medicinal plants. ‘phytochemdb’ is available for free at https://phytochemdb.com/.

Green synthesis of various saturated S-heterocyclic scaffolds: an update

Development of reliable and eco-friendly novel schemes for the synthesis of organic compounds is an important step in the field of organic and medicinal chemistry. Green chemistry-based strategies involving use of catalysts, green solvents, atom economic reactions etc. play a key role because of their exceptional ability to minimize the toxicity or hazards of the side products and processes. With the use of these green techniques, a number of researchers were able to synthesis a wide range of heterocyclic compounds. This chapter highlights the potential and diverse biological activities of saturated sulphur containing heterocyclic compounds including thiirane, thiane, thiolane and many more. The aim of this chapter is to provide fresh perspective on the various techniques employed for the formation of C–S bond by summarizing all green synthesis from 2016 to 2021.

Interdisciplinary analysis of drugs: Structural features and clinical data

Background:

Chemical structure is a vital consideration early in the drug development process. Its role in analysis of safety and efficacy is relatively diminished after drugs are approved for clinical use. This interdisciplinary study explores a strategy by which readily available clinical data may be used along with structural features of drugs to identify associations with potential utility for both clinical decision-making and drug development.

Methods:

Chemical functional groups and structural groups (SGs) of 261 drugs were manually classified in tiers, and their incidence of gastrointestinal (GI) and central nervous system (CNS) adverse drug reactions (ADRs) were obtained from a clinical database. Drugs with an GI or CNS ADR incidence of at least 10% were analyzed for correlations with their functional and SGs.

Results:

Eight statistically significant associations were detected by preliminary analysis: piperazine and methylene groups were associated with higher rate of CNS ADRs; while amides, secondary alcohols, and di-substituted phenyl groups were associated with lower rates of GI or CNS ADRs or both.

Conclusions:

Although further study is necessary to understand these associations and build upon this strategy, this exploratory analysis establishes a methodology by which chemical properties of drugs may be used to aid in clinical decision-making when choosing between otherwise equivalent drug therapy options, as the presence of specific groups on drugs may be associated with increased or decreased risks of specific ADRs.

Improving Small-Molecule Force Field Parameters in Ligand Binding Studies

Small molecules are major players of many chemical processes in diverse fields, from material science to biology. They are made by a combination of carbon and heteroatoms typically organized in system-specific structures of different complexity. This peculiarity hampers the application of standard force field parameters and their in silico study by means of atomistic simulations. Here, we combine quantum-mechanics and atomistic free-energy calculations to achieve an improved parametrization of the ligand torsion angles with respect to the state-of-the-art force fields in the paradigmatic molecular binding system benzamidine/trypsin. Funnel-Metadynamics calculations with the new parameters greatly reproduced the high-resolution crystallographic ligand binding mode and allowed a more accurate description of the binding mechanism, when the ligand might assume specific conformations to cross energy barriers. Our study impacts on future drug design investigations considering that the vast majority of marketed drugs are small-molecules.

Discovery of a Novel Potent and Selective Calcium Release-Activated Calcium Channel Inhibitor: 2,6-Difluoro-N-(2'-methyl-3'-(4-methyl-5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)-[1,1'-biphenyl]-4-yl)benzamide. Structure-Activity Relationship and Preclinical Characterization

The role of calcium release-activated calcium (CRAC) channels is well characterized and is of particular importance in T-cell function. CRAC channels are involved in the pathogenesis of several autoimmune diseases, making it an attractive therapeutic target for treating inflammatory diseases, like rheumatoid arthritis (RA). A systematic structure-activity relationship study with the goal of optimizing lipophilicity successfully yielded two lead compounds, 36 and 37. Both compounds showed decent potency and selectivity and a remarkable pharmacokinetic profile. Further characterization in in vivo RA models and subsequent histopathological evaluation of tissues led to the identification of 36 as a clinical candidate. Compound 36 displayed an excellent safety profile and had a sufficient safety margin to qualify it for use in human testing. Oral administration of 36 in Phase 1 clinical study in healthy volunteers established favorable safety, tolerability, and good target engagement as measured by levels of IL-2 and TNF-α.

The Chosen Few: Parallel Library Reaction Methodologies for Drug Discovery

Parallel library synthesis is an important tool for drug discovery because it enables the synthesis of closely related analogues in parallel via robust and general synthetic transformations. In this perspective, we analyzed the synthetic methodologies used in >5000 parallel libraries representing 15 prevalent synthetic transformations. The library data set contains complex substrates and diverse arrays of building blocks used over the last 14 years at AbbVie. The library synthetic methodologies that have demonstrated robustness and generality with proven success are described along with their substrate scopes. The evolution of the synthetic methodologies for library synthesis over the past decade is discussed. We also highlight that the combination of parallel library synthesis with high-throughput experimentation will continue to facilitate the discovery of library-amenable synthetic methodologies in drug discovery.

Synthesis, Characterization, and Biological Study of 3-Trifluoromethylpyrazole Tethered Chalcone-Pyrrole and Pyrazoline-Pyrrole Derivatives

The present study illustrates the design and synthesis of new series of 3-trifluoromethylpyrazole tethered chalcone-pyrrole and pyrazoline-pyrrole derivatives. All compounds were further screened for in vitro cytostatic activities on full NCI 60 cancer cell lines at National Cancer Institute, USA. Compounds (2E)-3-(1H-pyrrol-2-yl)-1-{4-[3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}prop-2-en-1-one (5a) and (2E)-1-{3-methyl-4-[3-(trifluoromethyl)-1H-pyrazol-1-yl]phenyl}-3-(1H-pyrrol-2-yl)prop-2-en-1-one (5c) displayed significant antiproliferative activity (Growth Percentage: -77.10 and -92.13, respectively at 10 μM concentration) against the UO-31 cell lines from renal cancer and were further selected for assay at 10-fold dilutions of five different concentrations (10^-4 to 10^-8  M). Both compounds 5a and 5c exhibited promising antiproliferative activity (GI₅₀ : 1.36 to 0.27 μM) against leukemia cancer cell lines HL-60 and RPMI-8226, colon cancer cell lines KM-12; breast cancer cell lines BT-549. Moreover, both compounds 5a and 5c were found to be non-cytotoxic (LC₅₀ >100) against HL-60, RPMI-8226, and KM-12 cell lines. Remarkably, GI₅₀ values of compounds 5a and 5c were identified as more promising than sunitinib against most cancer cell lines. In silico study of compounds 5a and 5c exemplified the desired ADME properties for drug-likeness as well as tighter interactions with VEGFR-2. Hence, compounds 5a and 5c would be good cytotoxic agents after further clinical study.

Maximizing the Oral Bioavailability of Poorly Water-Soluble Drugs Using Novel Oil-Like Materials in Lipid-Based Formulations

Lipid-based formulations, such as self-microemulsifying drug-delivery systems (SMEDDSs), are promising tools for the oral delivery of poorly water-soluble drugs. However, failure to maintain adequate aqueous solubility after coming into contact with gastrointestinal fluids is a major drawback. In this study, we examined the use of a novel cinnamic acid-derived oil-like material (CAOM) that binds drugs with a high affinity through π-π stacking and hydrophobic interactions, as an oil core in a SMEDDS for the oral delivery of fenofibrate in rats. The use of the CAOM in the SMEDDS resulted in an unprecedented enhancement in fenofibrate bioavailability, which exceeded the bioavailability values obtained using SMEDDSs based on corn oil, a conventional triglyceride oil, or Labrasol, an enhancer of intestinal permeation. Further characterization revealed that the CAOM SMEDDS does not alter the intestinal permeability and has no inhibitory activity on P-glycoprotein-mediated drug efflux. The results reported herein demonstrate the strong potential of CAOM formulations as new solubilizers for the efficient and safe oral delivery of drugs that have limited water solubility.

An overview of therapeutic anticancer drug monitoring based on surface enhanced (resonance) Raman spectroscopy (SE(R)RS)

Therapeutic drug monitoring (TDM) is important for many therapeutic regimens and has particular relevance for anticancer drugs which often have serious effects and whose optimum dosage can vary significantly between different patients. Many of the features of surface enhanced (resonance) Raman spectroscopy (SE(R)RS) suggest it should be very suitable for TDM of anticancer drugs and some initial studies which explore the potential of SE(R)RS for TDM of anticancer drugs have been published. This review brings this work together in an attempt to draw some general observations about key aspects of the approach, including the nature of the substrate used, matrix interference effects and factors governing adsorption of the target molecules onto the enhancing surface. There is now sufficient evidence to suggest that none of these pose real difficulties in the context of TDM. However, some issues, particularly the need to carry out multiplex measurements for TDM of combination therapies, have yet to be addressed.

Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules

The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.

Noncovalent Association and Partitioning of Some Perfume Components at Infinite Dilution with Myelin Basic Protein Pseudophase in Normal Saline

Myelin basic protein (MBP), one of the major protein constituents of the myelin sheath, possesses unique ligand-binding features. We present a novel equilibrium headspace gas chromatographic technique to examine the thermodynamics of noncovalent interactions between common perfume components: Lilial, Hedione, Hexylcinnamic aldehyde, and Versalide with MBP monomers and its hexameric MBP-pseudophase. A general theoretical model is used to calculate the critical aggregation concentration (cac) of MBP, perfume component binding constants with monomeric MBP, K₁₁, and MBP as pseudophase, K_n1, and free energies for perfume component binding with monomeric MBP, ΔG_b,11, and MBP as pseudophase, ΔG_b,n1. In addition, the pseudophase-water partition coefficients, K_x, the free energies of transfer of perfume from bulk water to the MBP-pseudophase, ΔG_t, and the intra-aggregate activity coefficients, γ_m^∞, at infinite dilution were also determined. The cac value measured by the method of fractional distribution is a unique and precise approach in understanding the aggregation phenomenon. Within the experimental error, the 1:1 binding free energies did not differ by more than 1 kJ/mol among the perfume components but favored the MBP pseudophase binding by 6 kJ/mol. Therefore, that protein aggregation can enhance the binding of small molecules is probably a general conclusion. While the magnitudes of K₁₁, K_n1, ΔG_b, K_x, and ΔG_t show weak trends, the γ_m^∞ values show a strong and distinct trend in interaction, spanning 4 orders of magnitude among the perfume components.

Are Structurally Modified Galactomannan Derivatives Biologically Active?

Galactomannans are versatile macromolecules with broad industrial potential. The influence of changes in the chemical structures and respective bioactivities of these polysaccharides have been extensively studied. The derivatives obtained by sulfation, complexation, and phosphorylation are the most studied biological properties in galactomannans. The derivatives obtained have shown several pharmacological activities such as antiviral, antimicrobial, anticoagulant, fibrinolytic, chemopreventive, anticancer, antioxidant, chondroprotective, analgesic, immunomodulatory, and antileishmanial. Considering the relevance of these studies, we aim to provide an overview of studies that apply galactomannan modification or derivatization strategies to improve their properties for applications in the biomedical area. We identified the success of most modified galactomannans for pharmacological purposes. However, some studies found loss of bioactivity of the original polysaccharide after chemical changes to its original structures.

Selective separation of amines from continuous processes using automated pH controlled extraction

An automated separation system is described for identifying the optimal conditions for purifying an amine from a mixture.

Piperazine-substituted derivatives of favipiravir for Nipah virus inhibition: What do in silico studies unravel?

Favipiravir is found to show excellent in-vitro inhibition activity against Nipah virus. To explore the structure-property relationship of Favipiravir, in silico designing of a series of piperazine substituted Favipiravir derivatives are attempted and computational screening has been done to evaluate its bimolecular interactions with Nipah virus. The geometrical features of all the molecules have been addressed from Density Functional Theory calculations. Chemical reactivity descriptor analysis was carried out to understand various reactivity parameters. The drug-likeness properties were estimated by a detailed ADMET study. The binding ability and the mode of binding of these derivatives into the Nipah virus are obtained from molecular docking studies. Our calculations show greater binding ability for the designed inhibitors compared to that of the experimentally reported molecule. Overall, the present work proves to offers new insights and guidelines for synthetic chemists to develop new drugs using piperazine substituted Favipiravir in the treatment of Nipah virus.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42452-020-04051-9.

Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis

Background

Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking.

Methods

Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA).

Results

Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and saponins all had bioactivity scores between −5.0 and 0.0 with respect to various receptor proteins and target enzymes. Solanidine, solasodine and solamargine had positive values of druglikeness which indicated that these compounds have the potential for development into future anticancer drugs. Toxicity potential evaluation revealed that glycoalkaloids and saponins had no toxicity, tumorigenicity or irritant effect(s). SAR analysis revealed that the number, type and location of sugar or the substitution of hydroxyl group on alkaloid backbone had an effect on the activity and that the presence of α-L-rhamnopyranose sugar at C-2 was critical for a compound to exhibit anticancer activity.

Conclusion

The present study revealed some cytoskeletal target(s) for S. nigrum phytoconstituents by docking analysis that have not been previously reported and thus warrant further investigations both in vitro and in vivo.

Ruthenium-catalyzed Bis-Homo-Diels-Alder reaction: searching for commercially available catalysts and expanding the scope of reaction

Commercially available ruthenium catalyst, Cp*RuCl(COD), was found to be active in catalyzing Bis-Homo-Diels-Alder [2+2+2] cycloaddition reactions between 1,5-cyclooctadiene and various alkynes giving moderate to good yields (35%–92%). The presence of electron donating groups, especially hydroxyl groups, greatly enhanced the reactivity of the alkyne moiety in the cycloaddition. The reaction was also found to be successful even in the presence of bulky substituents on the alkynes.

Ethnomedicine Claim Directed in Silico Prediction of Anticancer Activity

BACKGROUND

The merits of ethnomedicine-led approach to identify and prioritize anticancer medicinal plants have been challenged as cancer is more likely to be poorly understood in traditional medicine practices. Nonetheless, it is also believed that useful data can be generated by combining ethnobotanical findings with available scientific studies. Thus, this study combined an ethnobtanical study with ligand based in silico screening to identify relevant medical plants and predict their anticancer potential based on their phytoconstiutents reported in scientific literatures.

METHODS

First, relevant medicinal plants were identified through an ethnobotanical survey. A list of phytochemicals was prepared based on literature review of articles which reported on the natural products of identified medicinal plants. Then, their phytochemicals were subjected to in silico evaluation, which included a hybrid score similarity measure, rule of five, Ghose-Viswanadhan-Wendoloski (GVW)-indices and structural features criteria, to predict their anticancer activity and drugability.

RESULTS

A total of 18 medicinal plants and 265 phytoconstituents were identified. The natural product pool constituted 109(41.13%) terpenoids, 67(25.28%) phenolics, 29(10.94%) simple and functionalized hydrocarbons, 26(9.81%) alkaloids, 25(9.43%) glycosides and 9(3.40%) compounds belonging to different phytochemical classes. The similarity measure using CDRUG identified 34(12.73%) phytochemicals with high (p-Value < 0.05) and 35(13.21%) with moderate possibility (p-Value < 0.1) of anticancer activity. In fact, three of the predicted compounds had the same structure with known anticancer compounds (HSCORE=1). The 80% GVW-indices based antineoplastic drugabilityranges were all mate by 25 of the predicted compounds. Predicted compounds were also shown to have ring structures and functional groups deemed important for anticancer activity.

CONCLUSIONS

Given the findings, there is a promising anticancer activity by the traditionally used medicinal plants and a potential for the predicted phytochemicals to be pursued as possible hits or me-too drugs.