Combinatorial design and virtual screening of potent anti-tubercular fluoroquinolone and isothiazoloquinolone compounds utilizing QSAR and pharmacophore modelling

Primary Tuberculosis of Buccal and Labial Mucosa: Literature Review and a Rare Case Report of a Public Health Menace

Tuberculosis (TB) is a chronic granulomatous infectious disorder, caused by Mycobacterium tuberculosis. Despite the recent advancements in antitubercular therapy (ATT), it remains a global public health concern. TB is a leading infectious cause of global mortality, second only to coronavirus disease 2019 (COVID-19). TB of the oral cavity is an uncommon occurrence and may be classified as a primary and secondary form. The primary tubercular lesions are extremely rare, as the intact oral squamous epithelium resists the entry of tubercle bacilli. The commonest oral TB lesion is solitary ulceration with undermined edges, usually on the tongue, that does not exhibit healing with conservative therapies. Owing to the atypical presentation, the oral TB lesions often go unnoticed during clinical examination; hence, an oral physician should be familiar with the various oral manifestations of TB. A timely diagnosis coupled with interdisciplinary treatment is the key to combat disease dissemination. This manuscript aims to report a rare case of primary tuberculosis of the buccal and labial mucosa in a 43-year-old immunocompetent male patient. Buccal and labial mucosa are the infrequently affected sites for primary oral TB lesions. A detailed literature search carried out on the Google Scholar and PubMed search engines revealed only fifteen case reports and two case series of primary tuberculosis of the buccal mucosa and labial mucosa.

Molecular docking-based interaction studies on imidazo[1,2-a] pyridine ethers and squaramides as anti-tubercular agents

Development of new anti-tubercular agents is required in the wake of resistance to the existing and newly approved drugs through novel-validated targets like ATP synthase, etc. The major limitation of poor correlation between docking scores and biological activity by SBDD was overcome by a novel approach of quantitatively correlating the interactions of different amino acid residues present in the target protein structure with the activity. This approach well predicted the ATP synthase inhibitory activity of imidazo[1,2-a] pyridine ethers and squaramides (r = 0.84) in terms of Glu65b interactions. Hence, the models were developed on combined (r = 0.78), and training (r = 0.82) sets of 52, and 27 molecules, respectively. The training set model well predicted the diverse dataset (r = 0.84), test set (r = 0.755), and, external dataset (r_ext = 0.76). This model predicted three compounds from a focused library generated by incorporating the essential features of the ATP synthase inhibition with the pIC₅₀ values in the range of 0.0508-0.1494 µM. Molecular dynamics simulation studies ascertain the stability of the protein structure and the docked poses of the ligands. The developed model(s) may be useful in the identification and optimization of novel compounds against TB.

High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery

Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.

Discovery of Novel Inhibitors of Bacterial DNA Gyrase Using a QSAR-Based Approach

Type II topoisomerases like DNA gyrase initiate ATP-dependent negative supercoils in bacterial DNA. It is critical in all of the bacteria but is missing from eukaryotes, making it a striking target for antibacterials. Ciprofloxacin is a clinically approved drug, but its clinical effectiveness is affected by the emergence of resistance in both Gram-positive and Gram-negative bacteria. Thus, it is vital to identify novel compounds that can efficiently inhibit DNA gyrase, and quantitative structure-activity relationship (QSAR) modeling is a quick and economical means to do so. A QSAR-based virtual screening approach was applied to identify new gyrase inhibitors using an in-house-generated combinatorial library of 29828 compounds from seven ciprofloxacin scaffold structures. QSAR was built using a data set of 271 compounds, which were identified as positive and negative inhibitors from existing data reported in in vitro studies. The best QSAR model was developed using the 5-fold cross-validation Neural Network in Orange, and it was based on five PaDEL descriptors with an accuracy and sensitivity of 83%. As a result of screening of an in-house-built combinatorial library with the best-developed QSAR model, 675 compounds were identified as potential inhibitors of DNA gyrase. These inhibitors were further docked with DNA gyrase using AutoDock to compare the binding mode and score of the selected/screened compounds, and 615 compounds exhibited a docking score comparable to or lower than that of ciprofloxacin. Out of these, the top five analogues 902b, 9699f, 4419f, 5538f, and 898b reported in our study have binding scores of -13.81, -12.95, -12.52, -12.43, and -12.41 kcal/mol, respectively. The MD simulations of these five analogues for 100 ns supported the interaction stability of analogues with Escherichia coli DNA gyrase. Ninety-one per cent of the analogues screened by the QSAR model displayed better binding energy than ciprofloxacin, demonstrating the efficacy of the generated model. The NN-QSAR model proposed in this manuscript can be downloaded from https://github.com/ritu225/NN-QSAR_model.git.

Molecular docking-based interactions in QSAR studies on Mycobacterium tuberculosis ATP synthase inhibitors

Tuberculosis (TB) is a global threat with a large burden across the continents in terms of mortality, morbidity, and financial losses. The disease has evolved into multi-drug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) tuberculosis owing to numerous factors ranging from patients' non-compliance to demographical implications. There have been very few new drugs for resistant TB. Resistance has already been reported even for the newly introduced drug bedaquiline. An attempt has been made to integrate both structure-based and QSAR drug design techniques (QSAR-SBDD) for the identification of novel leads. The docking scores normally do not correlate with the activity. Hence, the docking results have been analysed in terms of the number of interactions rather than docking scores. The parameters derived from interactions have been used in developing the QSAR models. The best model shows a good correlation (r = 0.908) between the activity and interaction parameter 'C' describing the sum of all the interactions with each amino acid residue. This model also predicts external dataset with a good correlation (r_ext = 0.851) and can be used for the identification of novel chemical entities (NCEs) and repurposed drugs for TB therapeutics.

Insights into the molecular properties underlying antibacterial activity of prenylated (iso)flavonoids against MRSA

High resistance towards traditional antibiotics has urged the development of new, natural therapeutics against methicillin-resistant Staphylococcus aureus (MRSA). Prenylated (iso)flavonoids, present mainly in the Fabaceae, can serve as promising candidates. Herein, the anti-MRSA properties of 23 prenylated (iso)flavonoids were assessed in-vitro. The di-prenylated (iso)flavonoids, glabrol (flavanone) and 6,8-diprenyl genistein (isoflavone), together with the mono-prenylated, 4'-O-methyl glabridin (isoflavan), were the most active anti-MRSA compounds (Minimum Inhibitory Concentrations (MIC) ≤ 10 µg/mL, 30 µM). The in-house activity data was complemented with literature data to yield an extended, curated dataset of 67 molecules for the development of robust in-silico prediction models. A QSAR model having a good fit (R²_adj 0.61), low average prediction errors and a good predictive power (Q²) for the training (4% and Q²_LOO 0.57, respectively) and the test set (5% and Q²_test 0.75, respectively) was obtained. Furthermore, the model predicted well the activity of an external validation set (on average 5% prediction errors), as well as the level of activity (low, moderate, high) of prenylated (iso)flavonoids against other Gram-positive bacteria. For the first time, the importance of formal charge, besides hydrophobic volume and hydrogen-bonding, in the anti-MRSA activity was highlighted, thereby suggesting potentially different modes of action of the different prenylated (iso)flavonoids.

Current Computational Approaches for the Development of Anti-HIV Inhibitors: An Overview

BACKGROUND

Today, HIV-1 infection has become an extensive problem to public health and a greater challenge to all working researchers throughout the world. Since the beginning of HIV-1 virus, several antiviral therapeutic agents have been developed at various stages to combat HIV-1 infection. But, many of antiviral drugs are on the platform of drug resistance and toxicology issues, needs an urgent constructive investigation for the development of productive and protective therapeutics to make an improvement of individual life suffering with viral infection. As developing a novel agent is very costly, challenging and time taking route in the recent times.

METHODS

The review summarized about the modern approaches of computational aided drug discovery to developing a novel inhibitor within a short period of time and less cost.

RESULTS

The outcome suggests on the premise of reported information that the computational drug discovery is a powerful technology to design a defensive and fruitful therapeutic agents to combat HIV-1 infection and recover the lifespan of suffering one.

CONCLUSION

Based on survey of the reported information, we concluded that the current computational approaches is highly supportive in the progress of drug discovery and controlling the viral infection.

Use of Molecular Dynamics Simulations in Structure-Based Drug Discovery

BACKGROUND

Traditional drug discovery is a lengthy process which involves a huge amount of resources. Modern-day drug discovers various multidisciplinary approaches amongst which, computational ligand and structure-based drug designing methods contribute significantly. Structure-based drug designing techniques require the knowledge of structural information of drug target and drug-target complexes. Proper understanding of drug-target binding requires the flexibility of both ligand and receptor to be incorporated. Molecular docking refers to the static picture of the drug-target complex(es). Molecular dynamics, on the other hand, introduces flexibility to understand the drug binding process.

OBJECTIVE

The aim of the present study is to provide a systematic review on the usage of molecular dynamics simulations to aid the process of structure-based drug design.

METHOD

This review discussed findings from various research articles and review papers on the use of molecular dynamics in drug discovery. All efforts highlight the practical grounds for which molecular dynamics simulations are used in drug designing program. In summary, various aspects of the use of molecular dynamics simulations that underline the basis of studying drug-target complexes were thoroughly explained.

RESULTS

This review is the result of reviewing more than a hundred papers. It summarizes various problems that use molecular dynamics simulations.

CONCLUSION

The findings of this review highlight how molecular dynamics simulations have been successfully implemented to study the structure-function details of specific drug-target complexes. It also identifies the key areas such as stability of drug-target complexes, ligand binding kinetics and identification of allosteric sites which have been elucidated using molecular dynamics simulations.

Biological Evaluation of Noscapine analogues as Potent and Microtubule-Targeted Anticancer Agents

In present investigation, an attempt was undertaken to modify the C-9 position of noscapine (Nos), an opium alkaloid to yield 9 -hydroxy methyl and 9 -carbaldehyde oxime analogues for augmenting anticancer potential. The synthesis of 9-hydroxy methyl analogue of Nos was carried out by Blanc reaction and 9-carbaldehyde oxime was engineered by oxime formation method and characterized using FT-IR, ¹H NMR, ¹³C NMR, mass spectroscopy, and so on techniques. In silico docking techniques informed that 9-hydroxy methyl and 9-carbaldehyde oxime analogues of Nos had higher binding energy score as compared to Nos. The IC50 of Nos was estimated to be 46.8 µM signficantly (P < 0.05) higher than 8.2 µM of 9-carbaldehyde oxime and 4.6 µM of 9-hydroxy methyl analogue of Nos in U87, human glioblastoma cells. Moreover, there was significant (P < 0.05) difference between the IC50 of 9-carbaldehyde oxime and 9-hydroxy methyl analogue of Nos. Consistent to in vitro cytotoxicity data, 9-hydroxy methyl analogue of Nos induced significantly (P < 0.05) higher degree of apoptosis of 84.6% in U87 cells as compared to 78.5% and 64.3% demonstrated by 9-carbaldehyde oxime and Nos, respectively. Thus the higher therapeutic efficacy of 9-hydroxy methyl analogue of Nos may be credited to higher solubility and inhibitory constant (K).

In silico study directed towards identification of the key structural features of GyrB inhibitors targeting MTB DNA gyrase: HQSAR, CoMSIA and molecular dynamics simulations

Mycobacterium tuberculosis DNA gyrase subunit B (GyrB) has been identified as a promising target for rational drug design against fluoroquinolone drug-resistant tuberculosis. In this study, we attempted to identify the key structural feature for highly potent GyrB inhibitors through 2D-QSAR using HQSAR, 3D-QSAR using CoMSIA and molecular dynamics (MD) simulations approaches on a series of thiazole urea core derivatives. The best HQSAR and CoMSIA models based on IC₅₀ and MIC displayed the structural basis required for good activity against both GyrB enzyme and mycobacterial cell. MD simulations and binding free energy analysis using MM-GBSA and waterswap calculations revealed that the urea core of inhibitors has the strongest interaction with Asp79 via hydrogen bond interactions. In addition, cation-pi interaction and hydrophobic interactions of the R₂ substituent with Arg82 and Arg141 help to enhance the binding affinity in the GyrB ATPase binding site. Thus, the present study provides crucial structural features and a structural concept for rational design of novel DNA gyrase inhibitors with improved biological activities against both enzyme and mycobacterial cell, and with good pharmacokinetic properties and drug safety profiles.

QSAR and molecular docking studies of lethal factor protease inhibitors against Bacillus anthracis

Bacillus anthracis is considered as a biological warfare agent because it is the causative agent of the serious infectious anthrax disease. Delay in treatment leads to lethal factor-mediated toxaemia which is very critical due to lack of therapeutic options. Consequently, attempts have been made to discover potent lethal factor (LF) protease inhibitors such as small-molecule synthetic 2-thio-1,3-thiazolidine-4-one (rhodanine) compounds. But computed descriptor-based quantitative structure-activity relationship (QSAR) and drug design studies on such aspect are poorly represented. Therefore, an attempt was made for developing QSAR models using structural descriptors for 1,3-thiazolidine-4-one compounds. The models were developed on a series of 49 LF protease inhibitors using the combination of constitutional, functional group, atom-centred fragment and molecular property descriptors. The best QSAR model included four variables, namely, C-040, nR05, GVWAI-80 and ALOGP that correlated well with the anti-LF protease activity with a good correlation coefficient (r = 0.870) of good statistical significance (F_{4, 29} = 14.09 (α = 0.001) F_{4, 29} = 6.19). This model was also validated and explained 58.1% of variances of the Bacillus anthracis inhibitory activities of the studied compounds with r²_pred = 0.710 which denotes external predictability. Finally, molecular docking was carried out to predict the mode of binding of some highly active congeneric compounds. It was shown that VAL 1403 is an important residue for phenyl ring. TYR 1456 and HIS 1418 are responsible for interaction with the rhodanine nucleus. Therefore, these residues are considered responsible for the inhibition of LF protease anthrax and can predict significant dimension of essential structural features of these inhibitors to evaluate, screen and help priorities of the synthesis of the candidates against anthrax bioterrorism.

QSAR-based investigation on antibiotics facilitating emergence and dissemination of antibiotic resistance genes: A case study of sulfonamides against mutation and conjugative transfer in Escherichia coli

Antibiotic resistance genes (ARGs), which are emerging environmental contaminants, have posed great threats to global public health. Although extensive efforts have been undertaken to investigate ARG pollution, little attention has been paid to the structural information of antibiotics when exploring their impact on the emergence and dissemination of ARGs. In this study, setting Escherichia coli (E. coli) as the test organism, the effects of sulfonamides (SAs) on growth, mutation frequency and conjugative transfer frequency were tested, and quantitative structure-activity relationship (QSAR) was used to quantitatively analyze the promotion of SAs on these biological effects and explore their possible mechanism. The constructed QSAR models reveal that SAs may increase expression of the FtsZ protein and pili in E. coli via binding to the SdiA protein, ultimately leading to SAs facilitation of growth, mutation frequency and conjugative transfer frequency. The results indicate that SAs can produce selective pressure on E. coli to promote the emergence and dissemination of ARGs. This study provides reference data for further investigation of the emergence and dissemination of ARGs under antibiotic exposure and a new perspective for the mechanistic exploration of ARG pollution.

Hybrid Design of Isonicotinic Acid Hydrazide Derivatives: Machine Learning Studies, Synthesis and Biological Evaluation of their Antituberculosis Activity

BACKGROUND

Tuberculosis (TB) is an infection disease caused by Mycobacterium tuberculosis (Mtb) bacteria. One of the main causes of mortality from TB is the problem of Mtb resistance to known drugs.

OBJECTIVE

The goal of this work is to identify potent small molecule anti-TB agents by machine learning, synthesis and biological evaluation.

METHODS

The On-line Chemical Database and Modeling Environment (OCHEM) was used to build predictive machine learning models. Seven compounds were synthesized and tested in vitro for their antitubercular activity against H37Rv and resistant Mtb strains.

RESULTS

A set of predictive models was built with OCHEM based on a set of previously synthesized isoniazid (INH) derivatives containing a thiazole core and tested against Mtb. The predictive ability of the models was tested by a 5-fold cross-validation, and resulted in balanced accuracies (BA) of 61-78% for the binary classifiers. Test set validation showed that the models could be instrumental in predicting anti- TB activity with a reasonable accuracy (with BA = 67-79 %) within the applicability domain. Seven designed compounds were synthesized and demonstrated activity against both the H37Rv and multidrugresistant (MDR) Mtb strains resistant to rifampicin and isoniazid. According to the acute toxicity evaluation in Daphnia magna neonates, six compounds were classified as moderately toxic (LD50 in the range of 10-100 mg/L) and one as practically harmless (LD50 in the range of 100-1000 mg/L).

CONCLUSION

The newly identified compounds may represent a starting point for further development of therapies against Mtb. The developed models are available online at OCHEM http://ochem.eu/article/11 1066 and can be used to virtually screen for potential compounds with anti-TB activity.