A Guide to In Silico Drug Design

Isomer-sourced structure iteration methods for in silico development of inhibitors: Inducing GTP-bound NRAS-Q61 oncogenic mutations to an "off-like" state

The NRAS-mutant subset of melanoma represent some of the most aggressive and deadliest types associated with poor overall survival. Unfortunately, for more than 40 years, no therapeutic agent directly targeting NRAS mutations has been clinically approved. In this work, based on microsecond scale molecular dynamics simulations, the effect of Q61 mutations on NRAS conformational characteristics is revealed at the atomic level. The GTP-bound NRAS-Q61R and Q61K mutations show a specific targetable pocket between Switch-II and α-helix 3 whereas the NRAS-Q61L non-polar mutation category shows a different targetable pocket. Moreover, a new isomer-sourced structure iteration method has been developed for the in silico design of potential inhibitor prototypes for oncogenes. We show the possibility of a designed prototype HM-387 to target activated NRAS-Q61R and that it can gradually induce the transition from the activated NRAS-Q61R to an "off-like" state.

High-throughput virtual screening of Streptomyces spp. metabolites as antiviral inhibitors against the Nipah virus matrix protein

Nipah virus (NiV) remains a significant global concern due to its impact on both the agricultural industry and human health, resulting in substantial economic and health consequences. Currently, there is no cure or commercially available vaccine for the virus. Therefore, it is crucial to prioritize the discovery of new and effective treatment options to prevent its continued spread. Streptomyces spp. are rich sources of metabolites known for their bioactivity against certain diseases; however, their potential as antiviral drugs against the Nipah virus remain unexplored. In this study, 6524 Streptomyces spp. metabolites were screened through in silico methods for their inhibitory effects against the Nipah virus matrix (NiV-M) protein, which assists in virion assembly of Nipah virus. Different computer-aided tools were utilized to carry out the virtual screening process: ADMET profiling revealed 913 compounds with excellent safety and efficacy profiles, molecular docking predicted the binding poses and associated docking scores of the ligands in their respective targets, MD simulations confirmed the binding stability of the top ten highest-scoring ligands in a 100 ns all-atom simulation, PCA elucidated simulation convergence, and MMPB(GB)SA calculations estimated the binding energies of the final candidate compounds and determined the key residues crucial for complex formation. Using in silico methods, we identified six metabolites targeting the main substrate-binding site and five targeting the dimerization site that exhibited excellent stability and strong binding affinity. We recommend testing these compounds in the next stages of drug development to confirm their effectiveness as therapeutic agents against Nipah virus.

Laboratory and physiological aspects of substitute metazoan models for in vivo pharmacotoxicological analysis

New methods are essential to characterize the performance of substitute procedures for detecting therapeutic action(s) of a chemical or key signal of toxicological events. Herein, it was discussed the applications and advantages of using arthropods, worms, and fishes in pharmacological and/or toxicology assessments. First of all, the illusion of similarity covers many differences between humans and mice, remarkably about liver injury and metabolism of xenobiotics. Using invertebrates, especially earthworms (Eisenia fetida), brine shrimps (Artemia salina, Daphnia magna), and insects (Drosophila melanogaster) and vertebrates as small fishes (Oryzias latipes, Pimephales promelas, Danio rerio) has countless advantages, including fewer ethical conflicts, short life cycle, high reproduction rate, simpler to handle, and less complex anatomy. They can be used to find contaminants in organic matters and water and are easier genetically engineered with orthologous-mutated genes to explore specific proteins involved in proliferative and hormonal disturbances, chemotherapy multidrug resistance, and carcinogenicity. As multicellular embryos, larvae, and mature organisms, they can be tested in bigger-sized replication platforms with 24-, 96-, or 384-multiwell plates as cheaper and faster ways to select hit compounds from drug-like libraries to predict acute, subacute or chronic toxicity, pharmacokinetics, and efficacy parameters of pharmaceutical, cosmetic, and personal care products. Meanwhile, sublethal exposures are designed to identify changes in reproduction, body weight, DNA damages, oxidation, and immune defense responses in earthworms and zebrafishes, and swimming behaviors in A. salina and D. rerio. Behavioral parameters also give specificities on sublethal effects that would not be detected in zebrafishes by OECD protocols.

The New Paradigm in Animal Testing - "3Rs Alternatives"

Regulatory studies have revolutionised over time. Today, the focus has shifted from animal toxicity testing to non-animal for regulatory safety testing. This move is in line with the international 3Rs (Replacement, Reduction, and Refinement) principle and has also changed the regulator's perspective. The 3R principle has stimulated changes in policy, regulations, and new approaches to safety assessment in drug development in many countries. The 3Rs approach has led to the discovery and application of new technologies and more human-relevant in vitro approaches that minimise the use of animals including non-human primates, in research and improve animal welfare. In 2016, the European Medicines Agency published the Guidelines on the principles of regulatory acceptance of 3Rs testing approaches, followed by a conceptual paper in 2023 to align with current 3R standards. Additionally, the United States Food and Drug Administration passed new legislation in 2023 that no longer requires all new human drugs to be tested on animals, which will change the current testing paradigm. This review paper provides the adoption of the 3Rs and the current regulatory perspective regarding their implementation.

Synthesis, anticancer activity, docking and computational studies of new pyridyl-glycosyl hybrids and acyclic analogs

New pyridine-O-glycosides and their acyclic nucleoside analogues were prepared by heterocyclization and glycosylation. The anticancer activity against HCT-116, HepG2 and MCF-7 human cancer cells and BJ-1 cell revealed that the galacto- and xylopyranosyl glycosides possessing 4-bromophenyl have superior cytotoxic activities against HepG2 cell while glycosides 7-9 resulted in superior cytotoxic activities regarding MCF-7 breast cell. In case of HCT-116 colorectal carcinoma cells, two products and the derived glycosides and acyclic analogues showed potent activities. The most potent compounds were investigated for their possible binding affinities to the active site of CDK2 enzyme via in silico molecular docking simulation in addition to computational studies. The results support the antiproliferative effect and elucidate the interactions of 3a and 8 with catalytic sites.

Investigational new drugs for the treatment of leishmaniasis

INTRODUCTION

Over the past 20 years, significant progress has been made in anti-leishmanial therapy. Three new drugs/formulations are available for the treatment of various forms of leishmaniasis, namely oral miltefosine, paromomycin and liposomal amphotericin B. However, these advances in drug development have added considerable complexity for clinicians including toxicity, emergence of resistance and decreased sensitivity of available drugs. The development of newer drugs with less toxicity and more efficacy is urgently needed.

AREAS COVERED

This review comprehensively examines the latest developments and current status of antileishmanial drugs for the treatment of leishmaniasis across the world. Several new investigational drugs that showed anti-leishmanial activity under in vitro or in vivo conditions and either underwent the phase-I/II clinical trials or are on the verge of entering the trials were reviewed. We also delve into the challenges of drug resistance and discuss the emergence of new and effective antileishmanial compounds.

EXPERT OPINION

The available treatments for leishmaniasis are limited in number, toxic, expensive, and demand extensive healthcare resources. Every available antileishmanial drug is associated with several disadvantages, such as drug resistance and toxicity or high cost. Miltefosine is potentially teratogenic. New antileishmanial drugs/treatment modalities are sorely needed for expanding future treatment options.

A Chronicle Review of In-Silico Approaches for Discovering Novel Antimicrobial Agents to Combat Antimicrobial Resistance

Antimicrobial resistance (AMR) poses a foremost threat to global health, necessitating innovative strategies for discovering antimicrobial agents. This review explores the role and recent advances of in-silico techniques in identifying novel antimicrobial agents and combating AMR giving few briefings of recent case studies of AMR. In-silico techniques, such as homology modeling, virtual screening, molecular docking, pharmacophore modeling, molecular dynamics simulation, density functional theory, integrated machine learning, and artificial intelligence, are systematically reviewed for their utility in discovering antimicrobial agents. These computational methods enable the rapid screening of large compound libraries, prediction of drug-target interactions, and optimization of drug candidates. The review discusses integrating in-silico approaches with traditional experimental methods and highlights their potential to accelerate the discovery of new antimicrobial agents. Furthermore, it emphasizes the significance of interdisciplinary collaboration and data-sharing initiatives in advancing antimicrobial research. Through a comprehensive discussion of the latest developments in in-silico techniques, this review provides valuable insights into the future of antimicrobial research and the fight against AMR.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01355-x.

Identification of novel dual-target 4-hydroxyphenylpyruvate dioxygenase & phytoene dehydrogenase inhibitors via multiple virtual screening

Two important plant enzymes are 4-hydroxyphenylpyruvate dioxygenase (HPPD; EC 1.13.11.27), which is necessary for biosynthesis of plastoquinone and tocopherols, and phytoene dehydrogenase (PDS; EC 1.3.99.26), which plays an important role in colour rendering. Dual-target proteins that inhibit pigment synthesis will prevent resistant weeds and improve the spectral characteristics of herbicides. This study introduces virtual screening of pharmacophores based on the complex structure of the two targets. A three-dimensional database was established by screening 1,492,858 compounds based on the Lipinski principle. HPPD&PDS dual-target receptor-ligand pharmacophore models were then constructed, and nine potential dual-target inhibitors were obtained through pharmacophore modeling, molecular docking, and molecular dynamics simulations. Ultimately, ADMET prediction software yielded three compounds with high potential as dual-target herbicides. The obtained nine inhibitors were stable when combined with both HPPD and PDS proteins. This study offers guidance for the development of HPPD&PDS dual-target inhibitors with novel skeletons.

In-silico binding affinity of a phage display library screened novel peptide against various FABPs

In accordance to the American Heart Association (AHA), cardiovascular diseases (CVDs) are the leading cause of death around the globe, causing more than 19.1 million deaths in 2020. Heart-type fatty acid binding protein (H-FABP) is required for the metabolism of fatty acids (FA) inside cardiomyocytes is reported as a biomarker for myocardial damage. As early as one hour after an Acute myocardial infarction (AMI), H-FABP can be used to detect myocardial ischemia. Thus, H-FABP based detection can reduce the burden on the emergency department. A peptide-based detection system can provide point-of-care diagnostics for CVDs. There is a lot of research being done on peptide-based detection, and it has a lot of potential to help with unmet medical diagnostic needs. A twelve (12) amino acid peptide has been discovered using Phage Display Library Screening. The affinity of peptide with H-FABP and other FABPs has been done using molecular docking and ADMET profile has been done. Molecular docking of small peptides against the target protein can play a crucial role in recognizing peptide binding sites and poses. The docking study was done using the HDOCK server and the visualization of the docked complex was done using Pymol and UCSF chimera. The molecular simulation study of three protein-peptide complexes were done which also validated the binding affinity of peptide with the proteins. The RMSD, RMSF and radius of gyration are also analyzed. The results indicate that H-FABP shows higher level of binding interaction with the peptide having bond length ranging from 2.3 to 3.4 Å. The screened peptide is suitable for H-FABP binding and can be used for prognosis purposes in the heart ischemic conditions.

Structural Characterization of Heat Shock Protein 90β and Molecular Interactions with Geldanamycin and Ritonavir: A Computational Study

Drug repositioning is an important therapeutic strategy for treating breast cancer. Hsp90β chaperone is an attractive target for inhibiting cell progression. Its structure has a disordered and flexible linker region between the N-terminal and central domains. Geldanamycin was the first Hsp90β inhibitor to interact specifically at the N-terminal site. Owing to the toxicity of geldanamycin, we investigated the repositioning of ritonavir as an Hsp90β inhibitor, taking advantage of its proven efficacy against cancer. In this study, we used molecular modeling techniques to analyze the contribution of the Hsp90β linker region to the flexibility and interaction between the ligands geldanamycin, ritonavir, and Hsp90β. Our findings indicate that the linker region is responsible for the fluctuation and overall protein motion without disturbing the interaction between the inhibitors and the N-terminus. We also found that ritonavir established similar interactions with the substrate ATP triphosphate, filling the same pharmacophore zone.

GSRF-DTI: a framework for drug-target interaction prediction based on a drug-target pair network and representation learning on a large graph

BACKGROUND

Identification of potential drug-target interactions (DTIs) with high accuracy is a key step in drug discovery and repositioning, especially concerning specific drug targets. Traditional experimental methods for identifying the DTIs are arduous, time-intensive, and financially burdensome. In addition, robust computational methods have been developed for predicting the DTIs and are widely applied in drug discovery research. However, advancing more precise algorithms for predicting DTIs is essential to meet the stringent standards demanded by drug discovery.

RESULTS

We proposed a novel method called GSRF-DTI, which integrates networks with a deep learning algorithm to identify DTIs. Firstly, GSRF-DTI learned the embedding representation of drugs and targets by integrating multiple drug association information and target association information, respectively. Then, GSRF-DTI considered the influence of drug-target pair (DTP) association on DTI prediction to construct a drug-target pair network (DTP-NET). Next, we utilized GraphSAGE on DTP-NET to learn the potential features of the network and applied random forest (RF) to predict the DTIs. Furthermore, we conducted ablation experiments to validate the necessity of integrating different types of network features for identifying DTIs. It is worth noting that GSRF-DTI proposed three novel DTIs.

CONCLUSIONS

GSRF-DTI not only considered the influence of the interaction relationship between drug and target but also considered the impact of DTP association relationship on DTI prediction. We initially use GraphSAGE to aggregate the neighbor information of nodes for better identification. Experimental analysis on Luo's dataset and the newly constructed dataset revealed that the GSRF-DTI framework outperformed several state-of-the-art methods significantly.

Computational Insights into Papaveroline as an In Silico Drug Candidate for Alzheimer's Disease via Fyn Tyrosine Kinase Inhibition

Alzheimer's disease (AD) poses a significant global health challenge, necessitating the exploration of novel therapeutic strategies. Fyn Tyrosine Kinase has emerged as a key player in AD pathogenesis, making it an attractive target for drug development. This study focuses on investigating the potential of Papaveroline as a drug candidate for AD by targeting Fyn Tyrosine Kinase. The research employed high-throughput virtual screening and QSAR analysis were conducted to identify compounds with optimal drug-like properties, emphasizing adherence to ADMET parameters for further evaluation. Molecular dynamics simulations to analyze the binding interactions between Papaveroline and Staurosporine with Fyn Tyrosine Kinase over a 200-ns period. The study revealed detailed insights into the binding mechanisms and stability of the Papaveroline-Fyn complex, showcasing the compound's potential as an inhibitor of Fyn Tyrosine Kinase. Comparative analysis with natural compounds and a reference compound highlighted Papaveroline's unique characteristics and promising therapeutic implications for AD treatment. Overall, the findings underscore Papaveroline's potential as a valuable drug candidate for targeting Fyn Tyrosine Kinase in AD therapy, offering new avenues for drug discovery in neurodegenerative diseases. This study contributes to advancing our understanding of molecular interactions in AD pathogenesis and paves the way for further research and development in this critical area.

The United States Food and Drug Administration's Platform Technology Designation to Expedite the Development of Drugs

Drug development costs can be significantly reduced if proven "platform" technologies are allowed to be used without having to validate their use. The most recent US Food and Drug Administration (FDA) guideline brings more clarity, as well as a greater focus on the most complex technologies that can now be used for faster drug development. The FDA has highlights the use of lipid nanoparticles (LNPs) to package and deliver mRNA vaccines, gene therapy, and short (2-20 length) synthetic nucleotides (siRNA). Additionally, monoclonal antibody cell development is targeted. The FDA provides a systematic process of requesting platform status to benefit from its advantages. It brings advanced science and rationality into regulatory steps for the FDA's approval of drugs and biologicals.

Molecular docking of antidiabetic molecules of libas (Spondias pinnata) fruit and prediction of their pharmacokinetic properties

Diabetes mellitus is one of the chronic metabolic disorders that affects more than 16 million Filipinos. Proper education, medical intervention, and a good lifestyle can help individuals control and manage this disease. Spondias pinnata is one of the underutilized crops in the Philippines that is well-known for its satisfactory flavor and medicinal properties, including its antidiabetic activity. The quest for a natural and effective drug to manage diseases is a continuous work in progress. Drug discovery and design is a tedious and expensive process. Computer-aided drug design guides the design and makes the process more efficient and less costly. Molecular docking was used to determine the potential antidiabetic compounds from the 48 reported compounds found in S. pinnata fruit. Seven compounds namely squalene (-9.1 kcal/mol), rutin (-9 kcal/mol), catechin (-8.7 kcal/mol), quercetin (-8.5 kcal/mol), tocopherol (-8.4 kcal/mol), myricetin (-8.4 kcal/mol), and ellagic acid (-8.3 kcal/mol) showed binding affinities comparable to those of pioglitazone, a standard drug, with peroxisome proliferator-activated receptor gamma (PPARγ). Tocopherol and catechin showed good ADMET properties. Among the two compounds, catechin passed the four filters for drug-likeness. Thus, catechin could be a potential compound for the development of antidiabetic drugs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00230-3.

Comparative In Vitro and In Silico Analyses of Phytochemicals From Butea monosperma for Wound-Healing Potential in Human Cells

Aim The objective of this study is to investigate the phytochemicals present in Butea monosperma and assess their potential for healing wounds using a computational comparative method. Materials and methods The phytochemical substances derived from B. monosperma were examined using a phytochemical test, Fourier-transform infrared (FTIR) spectroscopy, and gas chromatography-mass spectroscopy (GCMS). The chemical structures of these substances were investigated in silico using computational techniques to predict their wound-healing capacity. The molecular docking tests evaluate the binding strengths of the phytochemicals to specific proteins that play a major role in wound-healing mechanisms. The pharmacokinetic features of the substances were evaluated by analyzing their ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiles. Results The computer analysis found several phytochemicals from B. monosperma that bind strongly to the proteins for wound healing: compounds such as hexanoic acid, 2,7-dimethyloct-7-en-5-yn-4-yl ester, 1,3,5-pentanetriol, 3-methyl-, and 2-butyne-1,4-diol. The ADMET analysis indicated favorable pharmacokinetic properties for the majority of the identified compounds, with low predicted toxicity. Conclusion Based on the in silico analysis, the phytochemicals in B. monosperma possess significant potential for use in wound-healing applications. These findings required additional in vitro and in vivo studies to confirm the effectiveness and safety of these drugs for improving wound healing. This study emphasizes the potential of B. monosperma as a source of innovative medicinal substances for wound care.

Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A systematic review

BACKGROUND

In the search for better anticancer drugs, computer-aided drug design (CADD) techniques play an indispensable role in facilitating the lengthy and costly drug discovery process especially when natural products are involved. Anthraquinone is one of the most widely-recognized natural products with anticancer properties. This review aimed to systematically assess and synthesize evidence on the utilization of CADD techniques centered on the anthraquinone scaffold for cancer treatment.

METHODS

The conduct and reporting of this review were done in accordance to the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) 2020 guideline. The protocol was registered in the "International prospective register of systematic reviews" database (PROSPERO: CRD42023432904) and also published recently. The search strategy was designed based on the combination of concept 1 "CADD or virtual screening", concept 2 "anthraquinone" and concept 3 "cancer". The search was executed in PubMed, Scopus, Web of Science and MedRxiv on 30 June 2023.

RESULTS

Databases searching retrieved a total of 317 records. After deduplication and applying the eligibility criteria, the final review ended up with 32 articles in which 3 articles were found by citation searching. The CADD methods used in the studies were either structure-based alone (69%) or combined with ligand-based methods via parallel (9%) or sequential (22%) approaches. Molecular docking was performed in all studies, with Glide and AutoDock being the most popular commercial and public software used respectively. Protein data bank was used in most studies to retrieve the crystal structure of the targets of interest while the main ligand databases were PubChem and Zinc. The utilization of in-silico techniques has enabled a deeper dive into the structural, biological and pharmacological properties of anthraquinone derivatives, revealing their remarkable anticancer properties in an all-rounded fashion.

CONCLUSION

By harnessing the power of computational tools and leveraging the natural diversity of anthraquinone compounds, researchers can expedite the development of better drugs to address the unmet medical needs in cancer treatment by improving the treatment outcome for cancer patients.

An Overview of SARS-CoV-2 Potential Targets, Inhibitors, and Computational Insights to Enrich the Promising Treatment Strategies

The rapid spread of the SARS-CoV-2 virus has emphasized the urgent need for effective therapies to combat COVID-19. Investigating the potential targets, inhibitors, and in silico approaches pertinent to COVID-19 are of utmost need to develop novel therapeutic agents and reprofiling of existing FDA-approved drugs. This article reviews the viral enzymes and their counter receptors involved in the entry of SARS-CoV-2 into host cells, replication of genomic RNA, and controlling the host cell physiology. In addition, the study provides an overview of the computational techniques such as docking simulations, molecular dynamics, QSAR modeling, and homology modeling that have been used to find the FDA-approved drugs and other inhibitors against SARS-CoV-2. Furthermore, a comprehensive overview of virus-based and host-based druggable targets from a structural point of view, together with the reported therapeutic compounds against SARS-CoV-2 have also been presented. The current study offers future perspectives for research in the field of network pharmacology investigating the large unexplored molecular libraries. Overall, the present in-depth review aims to expedite the process of identifying and repurposing drugs for researchers involved in the field of COVID-19 drug discovery.

Anticonvulsant effect of (±) citronellal possibly through the GABAergic and voltage-gated sodium channel receptor interaction pathways: In vivo and in silico studies

This study aimed to investigate the anticonvulsant effects of citronellal (CIT) and possible underlying mechanisms through an isoniazid (INH)-induced seizure (convulsion) via in vivo and in silico studies. For this, convulsions were induced by the oral administration of INH (300 mg/kg) to the mice. The animals were treated orally with different doses of CIT (50, 100, and 200 mg/kg). Vehicle served as a negative control (NC), while diazepam (DZP) (2 mg/kg) and carbamazepine (CAR) (80 mg/kg) were provided (p.o.) as positive controls (PC). A combination therapy of CIT (middle dose) with DZP and CAR was also given to two separate groups of animals to estimate the synergistic or antagonistic effects. Molecular docking and visualization of ligand-receptor interactions are also estimated through different computational tools. The results of the in vivo study showed that CIT dose-dependently significantly (p < 0.05) exhibited a higher onset of seizures while reducing the frequency and duration of seizures in mice compared to the NC group. Besides these, in combination therapy, CIT significantly antagonized the activity of CAR and DZP, leading to a reduction in the onset of seizures and an increase in their frequency and duration compared to treatment with CAR and DZP alone. Additionally, molecular docking revealed that the CIT exhibited a moderate binding affinity (-5.8 kcal/mol) towards the GABAA receptor and a relative binding affinity (-5.3 kcal/mol) towards the voltage-gated sodium channel receptor by forming several bonds. In conclusion, CIT showed moderate anticonvulsant activity in INH-induced convulsion animals, possibly by enhancing GABAA receptor activity and inhibiting the voltage-gated sodium channel receptor.

Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases

Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.

From Flora to Pharmaceuticals: 100 new additions to angiosperms of Gafargaon subdistrict in Bangladesh and unraveling antidiabetic drug candidates targeting DPP4 through in silico approach

Addition to the angiosperm flora provides essential insights into the biodiversity of a region, contributing to ecological understanding and conservation planning. Gafargaon subdistrict under Mymensingh district in Bangladesh represents a diverse population of angiosperms with a multifaceted ecosystem that demands re-evaluation of the existing angiosperm diversity of Gafargaon to update the status of angiosperm taxa and facilitate their conservation efforts. With this endeavor, a total of 100 angiosperm taxa belonging to 90 genera and 46 families were uncovered as additional occurrence in Gafargaon. The species in the area showcased a variety of life forms, including 63 herbs, 14 shrubs, 14 trees, and 9 climbers. Among the recorded taxa, Chamaecostus cuspidatus (Nees & Mart.) C.D. Specht & D.W. Stev. was selected for antidiabetic drug design endeavor based on citation frequency and ethnomedicinal evidence. A total of 41 phytochemicals of C. cuspidatus were screened virtually, targeting the Dipeptidyl peptidase 4 protein through structure-based drug design approach, which unveiled two lead compounds, such as Tigogenin (-9.0 kcal/mol) and Diosgenin (-8.5 kcal/mol). The lead candidates demonstrated favorable pharmacokinetic and pharmacodynamic properties with no major side effects. Molecular dynamics simulation revealed notable stability and structural compactness of the lead compounds. Principal component analysis and Gibbs free energy landscape further supported the results of molecular dynamics simulation. Molecular mechanics-based MM/GBSA approach unraveled higher free binding energies of Diosgenin (-47.36 kcal/mol) and Tigogenin (-46.70 kcal/mol) over Alogliptin (-46.32 kcal/mol). The outcome of the present investigation would enrich angiosperm flora of Gafargaon and shed light on the role of C. cuspidatus to develop novel antidiabetic therapeutics to combat diabetes.

In Silico and Chromatographic Methods for Analysis of Biotransformation of Prospective Neuroprotective Pyrrole-Based Hydrazone in Isolated Rat Hepatocytes

In the current study, chromatographic and in silico techniques were applied to investigate the biotransformation of ethyl 5-(4-bromophenyl)-1-(2-(2-(2-hydroxybenzylidene) hydrazinyl)-2-oxoethyl)-2-methyl-1H-pyrrole-3-carboxylate (11b) in hepatocytic media. The initial chromatographic procedure was based on the employment of the conventional octadecyl stationary phase method for estimation of the chemical stability. Subsequently, a novel and rapid chromatographic approach based on a phenyl-hexyl column was developed, aiming to separate the possible metabolites. Both methods were performed on a Dionex 3000 ThermoScientific (ACM 2, Sofia, Bulgaria) device equipped with a diode array detector set up at 272 and 279 nm for analytes detection. An acetonitrile: phosphate buffer of pH 3.5: methanol (17:30:53 v/v/v) was eluted isocratically as a mobile phase with a 1 mL/min flow rate. A preliminary purification from the biological media was achieved by protein precipitation with methanol. A validation procedure was carried out, where the method was found to correspond to all ICH (Q2) and M10 set criteria. Additionally, an in silico-based approach with the online server BioTransformer 3.0 was applied in an attempt to predict the possible metabolites of the title compound 11b. It was hypothesized that four CYP450 isoforms (1A2, 2C9, 3A4, and 2C8) were involved in the phase I metabolism, resulting in the formation of 12 metabolites. Moreover, docking studies were conducted to evaluate the formation of stable complexes between 11b and the aforementioned isoforms. The obtained data indicated three metabolites as the most probable products, two of which (M9_11b and M10_11b) were synthesized by a classical approach for verification. Finally, liquid chromatography with a mass detector was implemented for comprehensive and summarized analysis, and the obtained results revealed that the metabolism of the 11b proceeds possibly with the formation of glucuronide and glycine conjugate of M11_11b.

Evaluation of novel compounds as anti-bacterial or anti-virulence agents

Antimicrobial resistance is a global threat, leading to an alarming increase in the prevalence of bacterial infections that can no longer be treated with available antibiotics. The World Health Organization estimates that by 2050 up to 10 million deaths per year could be associated with antimicrobial resistance, which would equal the annual number of cancer deaths worldwide. To overcome this emerging crisis, novel anti-bacterial compounds are urgently needed. There are two possible approaches in the fight against bacterial infections: a) targeting structures within bacterial cells, similar to existing antibiotics; and/or b) targeting virulence factors rather than bacterial growth. Here, for the first time, we provide a comprehensive overview of the key steps in the evaluation of potential new anti-bacterial and/or anti-virulence compounds. The methods described in this review include: a) in silico methods for the evaluation of novel compounds; b) anti-bacterial assays (MIC, MBC, Time-kill); b) anti-virulence assays (anti-biofilm, anti-quorum sensing, anti-adhesion); and c) evaluation of safety aspects (cytotoxicity assay and Ames test). Overall, we provide a detailed description of the methods that are an essential tool for chemists, computational chemists, microbiologists, and toxicologists in the evaluation of potential novel antimicrobial compounds. These methods are cost-effective and have high predictive value. They are widely used in preclinical studies to identify new molecular candidates, for further investigation in animal and human trials.

In Silico Structural Modeling and Binding Site Analysis of Cerebroside Sulfotransferase (CST): A Therapeutic Target for Developing Substrate Reduction Therapy for Metachromatic Leukodystrophy

Cerebroside sulfotransferase (CST) is emerging as an important therapeutic target to develop substrate reduction therapy (SRT) for metachromatic leukodystrophy (MLD), a rare neurodegenerative lysosomal storage disorder. MLD develops with progressive impairment and destruction of the myelin sheath as a result of accumulation of sulfatide around the nerve cells in the absence of its recycling mechanism with deficiency of arylsulfatase A (ARSA). Sulfatide is the product of the catalytic action of cerebroside sulfotransferase (CST), which needs to be regulated under pathophysiological conditions by inhibitor development. To carry out in silico-based preliminary drug screening or for designing new drug candidates, a high-quality three-dimensional (3D) structure is needed in the absence of an experimentally derived three-dimensional crystal structure. In this study, a 3D model of the protein was developed using a primary sequence with the SWISS-MODEL server by applying the top four GMEQ score-based templates belonging to the sulfotransferase family as a reference. The 3D model of CST highlights the features of the protein responsible for its catalytic action. The CST model comprises five β-strands, which are flanked by ten α-helices from both sides as well as form the upside cover of the catalytic pocket of CST. CST has two catalytic regions: PAPS (-sulfo donor) binding and galactosylceramide (-sulfo acceptor) binding. The catalytic action of CST was proposed via molecular docking and molecular dynamic (MD) simulation with PAPS, galactosylceramide (GC), PAPS-galactosylceramide, and PAP. The stability of the model and its catalytic action were confirmed using molecular dynamic simulation-based trajectory analysis. CST response against the inhibition potential of the experimentally reported competitive inhibitor of CST was confirmed via molecular docking and molecular dynamics simulation, which suggested the suitability of the CST model for future drug discovery to strengthen substrate reduction therapy for MLD.

Advances in structure-based drug design: The potential for precision therapeutics in psychiatric disorders

Over the years, the field of GPCR drug design has undergone a remarkable evolution, fueled by advancements in science and technology. This evolution has given rise to a diverse range of ideas and approaches in structure-based drug design, bolstering the versatility and strength of the GPCR drug design toolbox. This review encapsulates the iterative development process, navigating challenges and opportunities in structure-based drug design within GPCRs. With a focused emphasis on its impact on psychiatric disorders, the review accentuates recent advancements and delves into the potentials unlocked by emerging technologies. The review explores the intricate interplay between scientific progress and iterative refinement, offering profound insights into the potential pathways that lie ahead for GPCR drug design.

Harvesting phosphorus-containing moieties for their antibacterial effects

Clinically manifested resistance of bacteria to antibiotics has emerged as a global threat to society and there is an urgent need for the development of novel classes of antibacterial agents. Recently, the use of phosphorus in antibacterial agents has been explored in quite an unprecedent manner. In this comprehensive review, we summarize the use of phosphorus-containing moieties (phosphonates, phosphonamidates, phosphonopeptides, phosphates, phosphoramidates, phosphinates, phosphine oxides, and phosphoniums) in compounds with antibacterial effect, including their use as β-lactamase inhibitors and antibacterial disinfectants. We show that phosphorus-containing moieties can serve as novel pharmacophores, bioisosteres, and prodrugs to modify pharmacodynamic and pharmacokinetic properties. We further discuss the mechanisms of action, biological activities, clinical use and highlight possible future prospects.

Physical-chemical repurposing of drugs. History of its formation in Russia

It is reported that the traditional scheme of finding and developing a new drug and conducting the whole complex of preclinical studies requires several thousand chemical compounds, hundreds of millions of US dollars and more than 12 years of work. It is shown that physicochemical pharmacology was born in Russia at the end of the 20th century, which in our days has been transformed into physicochemical repurposing of known medicines. The first successfully repurposed known drug was a solution of 4% potassium chloride, which had previously traditionally belonged to the group of macro- and microelements, used by intravenous injections to regulate acid-base balance and rhythmic activity of the heart. In 1983, it was stated that this medicinal solution, when heated to 3942C and applied topically by irrigation of the bleeding surface, could be classified as a vasoconstrictor and hemostatic drug. Hyperthermia was used as a physico-chemical reprofiling factor, which, according to the Arrhenius law, accelerated and intensified, on the one hand, the spastic action of K+ cations on the gaping blood vessels (formation of hyperkalium contracture in the smooth muscles of the vascular wall) and, on the other hand, the blood clotting process in the wound. In subsequent years, the promise of physicochemical repurposing of known drugs was shown on the example of water, hydrogen peroxide, sodium chloride and sodium bicarbonate by purposefully changing their temperature, acid, osmotic activity, as well as the amount and quality of gas content (passing). A chronology of the physicochemical repurposing of known drug solutions and tablets is described and the essence of such new groups of drugs as bleachers of bruises and pyolytics is given. It is shown that both groups of drugs were discovered in Russia and are intended for local use to bleach bruises (blood stains) and dissolve thick mucus, sputum, pus, blood clots, meconium and other dense biological tissues containing the enzyme catalase. It is pointed out that the advantage and at the same time the limitation of the known drugs repurposed according to this scheme is their local application, since their new pharmacological activity is caused mainly by the physical and chemical principle of action, which is manifested by local interaction with the selected area of the patients organism.

Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A protocol for systematic review

There is still unmet medical need in cancer treatment mainly due to drug resistance and adverse drug events. Therefore, the search for better drugs is essential. Computer-aided drug design (CADD) and discovery tools are useful to streamline the lengthy and costly drug development process. Anthraquinones are a group of naturally occurring compounds with unique scaffold that exert various biological properties including anticancer activities. This protocol describes a systematic review that provide insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment. It was prepared in accordance with the "Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 guidelines, and published in the "International prospective register of systematic reviews" database (PROSPERO: CRD42023432904). Search strategies will be developed based on the combination of relevant keywords and executed in PubMed, Scopus, Web of Science and MedRxiv. Only original studies that employed CADD as primary tool in virtual screening for the purpose of designing or discovering anti-cancer drugs involving anthraquinone scaffold published in English language will be included. Two independent reviewers will be involved to screen and select the papers, extract the data and assess the risk of bias. Apart from exploring the trends and types of CADD methods used, the target proteins of these compounds in cancer treatment will also be revealed in this review. It is believed that the outcome of this study could be utilized to support the ongoing research in similar area with better quality and greater probability of success, consequently optimizing the resources in subsequent in vitro, in vivo, non-clinical and clinical development. It will also serve as an evidence based scientific guide for new research to design novel anthraquinone-derived drug with improved efficacy and safety profile for cancer treatment.

Computational, In Vitro, and In Vivo Models for Nose-to-Brain Drug Delivery Studies

Direct nose-to-brain drug delivery offers the opportunity to treat central nervous system disorders more effectively due to the possibility of drug molecules reaching the brain without passing through the blood-brain barrier. Such a delivery route allows the desired anatomic site to be reached while ensuring drug effectiveness, minimizing side effects, and limiting drug losses and degradation. However, the absorption of intranasally administered entities is a complex process that considerably depends on the interplay between the characteristics of the drug delivery systems and the nasal mucosa. Various preclinical models (in silico, in vitro, ex vivo, and in vivo) are used to study the transport of drugs after intranasal administration. The present review article attempts to summarize the different computational and experimental models used so far to investigate the direct delivery of therapeutic agents or colloidal carriers from the nasal cavity to the brain tissue. Moreover, it provides a critical evaluation of the data available from different studies and identifies the advantages and disadvantages of each model.

A perspective on the sharing of docking data

Computational approaches are nowadays largely applied in drug discovery projects. Among these, molecular docking is the most used for hit identification against a drug target protein. However, many scientists in the field shed light on the lack of availability and reproducibility of the data obtained from such studies to the whole community. Consequently, sustaining and developing the efforts toward a large and fully transparent sharing of those data could be beneficial for all researchers in drug discovery. The purpose of this article is first to propose guidelines and recommendations on the appropriate way to conduct virtual screening experiments and second to depict the current state of sharing molecular docking data. In conclusion, we have explored and proposed several prospects to enhance data sharing from docking experiment that could be developed in the foreseeable future.

Catalytic resilience of multicomponent aromatic ring-hydroxylating dioxygenases in Pseudomonas for degradation of polycyclic aromatic hydrocarbons

Hydrophobic organic compounds, either natural or introduced through anthropogenic activities, pose a serious threat to all spheres of life, including humankind. These hydrophobic compounds are recalcitrant and difficult to degrade by the microbial system; however, microbes have also evolved their metabolic and degradative potential. Pseudomonas species have been reported to have a multipotential role in the biodegradation of aromatic hydrocarbons through aromatic ring-hydroxylating dioxygenases (ARHDs). The structural complexity of different hydrophobic substrates and their chemically inert nature demands the explicit role of evolutionary conserved multicomponent enzyme ARHDs. These enzymes catalyze ring activation and subsequent oxidation by adding two molecular oxygen atoms onto the vicinal carbon of the aromatic nucleus. This critical metabolic step in the aerobic mode of degradation of polycyclic aromatic hydrocarbons (PAHs) catalyzed by ARHDs can also be explored through protein molecular docking studies. Protein data analysis enables an understanding of molecular processes and monitoring complex biodegradation reactions. This review summarizes the molecular characterization of five ARHDs from Pseudomonas species already reported for PAH degradation. Homology modeling for the amino acid sequences encoding the catalytic α-subunit of ARHDs and their docking analyses with PAHs suggested that the enzyme active sites show flexibility around the catalytic pocket for binding of low molecular weight (LMW) and high molecular weight (HMW) PAH substrates (naphthalene, phenanthrene, pyrene, benzo[α]pyrene). The alpha subunit harbours variable catalytic pockets and broader channels, allowing relaxed enzyme specificity toward PAHs. ARHD's ability to accommodate different LMW and HMW PAHs demonstrates its 'plasticity', meeting the catabolic demand of the PAH degraders.