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1.
AAPS PharmSciTech ; 25(6): 152, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38954218

ABSTRACT

Bedaquiline (BQ) solid lipid nanoparticles (SLNs), which have previously been formulated for parenteral administration, have a risk of patient non-compliance in treating tuberculosis. This research presents a strategy to develop BQ SLNs for oral delivery to improve patient adherence, The upper and lower levels for the formulation excipients were generated from screening experiments. Using 4 input factors (BQ, lecithin, Tween 80, and PEG), a full factorial design from 3 × 2x2 × 2 experiments was randomly arranged to investigate 3 response variables: Particle size distribution (PSD), polydispersity index (PdI), and zeta potential (ZP). High shear homogenization was used to mix the solvent and aqueous phases, with 15% sucrose as a cryoprotectant. The response variables were assessed using a zeta sizer while TEM micrographs confirmed the PSD data. Solid-state assessments were conducted using powdered X-ray diffraction and scanning electron microscopy (SEM) imaging. A comparative invitro assessment was used to determine drug release from an equivalent dose of BQ free base powder and BQ-SLN, both packed in hard gelatin capsules. The sonicated formulations obtained significant effects for PSD, PdI, and ZP. The p-values (0.0001 for PdI, 0.0091 for PSD) for BQ as an independent variable in the sonicated formulation were notably higher than those in the unsonicated formulation (0.1336 for PdI, 0.0117 for PSD). The SEM images were between 100 - 400 nm and delineated nanocrystals of BQ embedded in the lipid matrix. The SLN formulation provides higher drug levels over the drug's free base; a similarity factor (f2 = 18.3) was estimated from the dissolution profiles.


Subject(s)
Chemistry, Pharmaceutical , Diarylquinolines , Lipids , Nanoparticles , Particle Size , Diarylquinolines/chemistry , Diarylquinolines/administration & dosage , Nanoparticles/chemistry , Lipids/chemistry , Chemistry, Pharmaceutical/methods , Excipients/chemistry , Drug Liberation , Antitubercular Agents/administration & dosage , Antitubercular Agents/chemistry , Drug Compounding/methods , X-Ray Diffraction/methods , Microscopy, Electron, Scanning/methods , Drug Carriers/chemistry , Administration, Oral , Liposomes
2.
Biomolecules ; 14(6)2024 Jun 16.
Article in English | MEDLINE | ID: mdl-38927114

ABSTRACT

Incidences of drug-resistant tuberculosis have become common and are rising at an alarming rate. Aminoacyl t-RNA synthetase has been validated as a newer target against Mycobacterium tuberculosis. Leucyl t-RNA synthetase (LeuRS) is ubiquitously found in all organisms and regulates transcription, protein synthesis, mitochondrial RNA cleavage, and proofreading of matured t-RNA. Leucyl t-RNA synthetase promotes growth and development and is the key enzyme needed for biofilm formation in Mycobacterium. Inhibition of this enzyme could restrict the growth and development of the mycobacterial population. A database consisting of 2734 drug-like molecules was screened against leucyl t-RNA synthetase enzymes through virtual screening. Based on the docking scores and MMGBSA energy values, the top three compounds were selected for molecular dynamics simulation. The druggable nature of the top three hits was confirmed by predicting their pharmacokinetic parameters. The top three hits-compounds 1035 (ZINC000001543916), 1054 (ZINC000001554197), and 2077 (ZINC000008214483)-were evaluated for their binding affinity toward leucyl t-RNA synthetase by an isothermal titration calorimetry study. The inhibitory activity of these compounds was tested against antimycobacterial activity, biofilm formation, and LeuRS gene expression potential. Compound 1054 (Macimorelin) was found to be the most potent molecule, with better antimycobacterial activity, enzyme binding affinity, and significant inhibition of biofilm formation, as well as inhibition of the LeuRS gene expression. Compound 1054, the top hit compound, has the potential to be used as a lead to develop successful leucyl t-RNA synthetase inhibitors.


Subject(s)
Antitubercular Agents , Enzyme Inhibitors , Leucine-tRNA Ligase , Molecular Docking Simulation , Mycobacterium tuberculosis , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Ligands , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Leucine-tRNA Ligase/antagonists & inhibitors , Leucine-tRNA Ligase/metabolism , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Calorimetry , Molecular Dynamics Simulation , Tuberculosis/drug therapy , Tuberculosis/microbiology , Computer Simulation , Protein Binding , Humans
3.
Bioorg Med Chem Lett ; 109: 129846, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38857850

ABSTRACT

Over the past 2000 years, tuberculosis (TB) has been responsible for more deaths than any other infectious disease. In recent years, there has been a recovery of research and development (R&D) efforts focused on TB drugs. This is driven by the pressing need to combat the global spread of the disease and develop improved therapies for both drug-sensitive and drug-resistant strains. Many new TB drug candidates have recently entered clinical trials, marking the beginning of a rebirth in this area after decades of neglect. The problem is that very few of the hundreds of compounds identified each year as potential anti-TB drugs really make it to the clinical development stage. This perspective focuses on the primary obstacles and approaches involved in the development of new medications for TB. This will help medicinal chemists better understand TB drug challenges and develop novel drug candidates.


Subject(s)
Antitubercular Agents , Drug Discovery , Mycobacterium tuberculosis , Tuberculosis , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Antitubercular Agents/chemical synthesis , Humans , Tuberculosis/drug therapy , Mycobacterium tuberculosis/drug effects , Microbial Sensitivity Tests , Molecular Structure
4.
Sci Rep ; 14(1): 14660, 2024 06 25.
Article in English | MEDLINE | ID: mdl-38918410

ABSTRACT

The emergence of drug-resistant Mycobacterium tuberculosis strains is a threat to global health necessitating the discovery of novel chemotherapeutic agents. Natural products drug discovery, which previously led to the discovery of rifamycins, is a valuable approach in this endeavor. Against this backdrop, we set out to investigate the in vitro antimycobacterial properties of medicinal plants from Ghana and South Africa, evaluating 36 extracts and their 252 corresponding solid phase extraction (SPE) generated fractions primarily against the non-pathogenic Mycobacterium smegmatis and Mycobacterium aurum species. The most potent fraction was further evaluated in vitro against infectious M. tuberculosis strain. Crinum asiaticum (bulb) (Amaryllidaceae) emerged as the most potent plant species with specific fractions showing exceptional, near equipotent activity against the non-pathogenic Mycobacterium species (0.39 µg/ml ≤ MIC ≤ 25 µg/ml) with one fraction being moderately active (MIC = 32.6 µg/ml) against M. tuberculosis. Metabolomic analysis led to the identification of eight compounds predicted to be active against M. smegmatis and M. aurum. In conclusion, from our comprehensive study, we generated data which provided an insight into the antimycobacterial properties of Ghanaian and South African plants. Future work will be focused on the isolation and evaluation of the compounds predicted to be active.


Subject(s)
Microbial Sensitivity Tests , Mycobacterium tuberculosis , Plant Extracts , Plants, Medicinal , Plants, Medicinal/chemistry , South Africa , Plant Extracts/pharmacology , Plant Extracts/chemistry , Ghana , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Mycobacterium/drug effects , Mycobacterium smegmatis/drug effects , Humans , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/chemistry
5.
Mar Drugs ; 22(6)2024 Jun 03.
Article in English | MEDLINE | ID: mdl-38921570

ABSTRACT

A new dimeric C-glycoside polyketide chrysomycin F (1), along with four new monomeric compounds, chrysomycins G (2), H (3), I (4), J (5), as well as three known analogues, chrysomycins A (6), B (7), and C (8), were isolated and characterised from a strain of Streptomyces sp. obtained from a sediment sample collected from the South China Sea. Their structures were determined by detailed spectroscopic analysis. Chrysomycin F contains two diastereomers, whose structures were further elucidated by a biomimetic [2 + 2] photodimerisation of chrysomycin A. Chrysomycins B and C showed potent anti-tuberculosis activity against both wild-type Mycobacterium tuberculosis and a number of clinically isolated MDR M. tuberculosis strains.


Subject(s)
Antitubercular Agents , Microbial Sensitivity Tests , Mycobacterium tuberculosis , Polyketides , Streptomyces , Streptomyces/chemistry , Streptomyces/metabolism , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Antitubercular Agents/isolation & purification , Polyketides/pharmacology , Polyketides/chemistry , Polyketides/isolation & purification , Glycosides/chemistry , Glycosides/pharmacology , Glycosides/isolation & purification , China , Molecular Structure , Anthraquinones/pharmacology , Anthraquinones/chemistry , Anthraquinones/isolation & purification
6.
Future Med Chem ; 16(10): 949-961, 2024.
Article in English | MEDLINE | ID: mdl-38910577

ABSTRACT

Aim: The WHO, Global tuberculosis report 2022 estimated number of tuberculosis (TB) cases reached 10.6 million in 2021, reflecting a 4.5% increase compared with the 10.1 million reported in 2020. The incidence rate of TB showed 3.6% rise from 2020 to 2021. Results/methodology: This manuscript discloses Cu-promoted single pot A3-coupling between triclosan (TCS)-based alkyne, formaldehyde and secondary amines to yield TCS-based Mannich adducts. Additionally, the coupling of TCS-alkynes in the presence of Cu(OAc)2 afforded the corresponding homodimers. Among tested compounds, the most potent one in the series 11 exhibited fourfold higher potency than rifabutin against drug-resistant Mycobacterium abscessus. The selectivity index was also substantially improved, being 26 (day 1) and 15 (day 3), which is four-times better than TCS.


[Box: see text].


Subject(s)
Copper , Microbial Sensitivity Tests , Triclosan , Triclosan/pharmacology , Triclosan/chemistry , Triclosan/chemical synthesis , Copper/chemistry , Copper/pharmacology , Molecular Structure , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Antitubercular Agents/chemical synthesis , Mycobacterium abscessus/drug effects , Computer Simulation , Structure-Activity Relationship , Humans , Mannich Bases/chemistry , Mannich Bases/pharmacology , Mannich Bases/chemical synthesis
7.
Drug Des Devel Ther ; 18: 1969-1979, 2024.
Article in English | MEDLINE | ID: mdl-38836115

ABSTRACT

Tuberculosis (TB) stands as the second most prevalent cause of global human mortality from infectious diseases. In 2022, the World Health Organization documented an estimated number of global TB cases reaching 7.5 million, which causes death for 1.13 million patients. The continuous growth of drug-resistant TB cases due to various mutations in the Mycobacterium tuberculosis (MTB) strain, raises the urgency of the exploration of novel anti-TB treatments. Ursolic acid (UA) is a natural pentacyclic triterpene found in various plants that has shown potential as a novel anti-TB agent. This review aims to provide an overview of the therapeutic prospects of UA against MTB, with a particular emphasis on in silico, in vitro, and in vivo studies. Various mechanisms of action of UA against MTB are briefly recapped from in silico studies, such as enoyl acyl carrier protein reductase inhibitors, FadA5 (Acetyl-CoA acetyltransferase) inhibitors, tuberculosinyl adenosine transferase inhibitors, and small heat shock protein 16.3 inhibitor. The potential of UA to overcome drug resistance and its synergistic effects with existing antituberculosis drugs are briefly explained from in vitro studies using a variety of methods, such as Microplate Alamar Blue Assay, Mycobacteria Growth Indicator Tube 960 and Resazurin Assays, morphological change evaluation using transmission electron microscopy, and in vivo studies using BALB/C infected with multi drug resistant clinical isolates. Besides its promising mechanism as an antituberculosis drug, its complex chemical composition, limited availability and supply, and lack of intellectual property are also reviewed as those are the most frequently occurring challenges that need to be addressed for the successful development of UA as novel anti-TB agent.


Subject(s)
Antitubercular Agents , Mycobacterium tuberculosis , Triterpenes , Ursolic Acid , Triterpenes/pharmacology , Triterpenes/chemistry , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Humans , Mycobacterium tuberculosis/drug effects , Animals , Microbial Sensitivity Tests , Tuberculosis/drug therapy , Tuberculosis/microbiology
8.
Molecules ; 29(11)2024 May 24.
Article in English | MEDLINE | ID: mdl-38893370

ABSTRACT

Kallopterolides A-I (1-9), a family of nine diterpenoids possessing either a cleaved pseudopterane or a severed cembrane skeleton, along with several known compounds were isolated from the Caribbean Sea plume Antillogorgia kallos. The structures and relative configurations of 1-9 were characterized by analysis of HR-MS, IR, UV, and NMR spectroscopic data in addition to computational methods and side-by-side comparisons with published NMR data of related congeners. An investigation was conducted as to the potential of the kallopterolides as plausible in vitro anti-inflammatory, antiprotozoal, and antituberculosis agents.


Subject(s)
Anthozoa , Diterpenes , Diterpenes/chemistry , Diterpenes/isolation & purification , Diterpenes/pharmacology , Animals , Anthozoa/chemistry , Antiprotozoal Agents/chemistry , Antiprotozoal Agents/pharmacology , Antiprotozoal Agents/isolation & purification , Caribbean Region , Molecular Structure , Anti-Inflammatory Agents/chemistry , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/isolation & purification , Magnetic Resonance Spectroscopy , Antitubercular Agents/chemistry , Antitubercular Agents/pharmacology , Antitubercular Agents/isolation & purification
9.
Bioorg Med Chem ; 108: 117774, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38833750

ABSTRACT

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), which remains a significant global health challenge. The emergence of multidrug-resistant (MDR) Mtb strains imposes the development of new therapeutic strategies. This study focuses on the identification and evaluation of potential inhibitors against Mtb H37Ra through a comprehensive screening of an in-house chemolibrary. Subsequently, a promising pyrimidine derivative (LQM495) was identified as promising and then further investigated by experimental and in silico approaches. In this context, computational techniques were used to elucidate the potential molecular target underlying the inhibitory action of LQM495. Then, a consensus reverse docking (CRD) protocol was used to investigate the interactions between this compound and several Mtb targets. Out of 98 Mtb targets investigated, the enhanced intracellular survival (Eis) protein emerged as a target for LQM495. To gain insights into the stability of the LQM495-Eis complex, molecular dynamics (MD) simulations were conducted over a 400 ns trajectory. Further insights into its binding modes within the Eis binding site were obtained through a Quantum mechanics (QM) approach, using density functional theory (DFT), with B3LYP/D3 basis set. These calculations shed light on the electronic properties and reactivity of LQM495. Subsequently, inhibition assays and kinetic studies of the Eis activity were used to investigate the activity of LQM495. Then, an IC50 value of 11.0 ± 1.4 µM was found for LQM495 upon Eis protein. Additionally, its Vmax, Km, and Ki parameters indicated that it is a competitive inhibitor. Lastly, this study presents LQM495 as a promising inhibitor of Mtb Eis protein, which could be further explored for developing novel anti-TB drugs in the future.


Subject(s)
Antitubercular Agents , Bacterial Proteins , Molecular Docking Simulation , Mycobacterium tuberculosis , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Structure-Activity Relationship , Microbial Sensitivity Tests , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/chemical synthesis , Molecular Structure , Acetyltransferases/antagonists & inhibitors , Acetyltransferases/metabolism , Dose-Response Relationship, Drug , Molecular Dynamics Simulation , Pyrimidines/chemistry , Pyrimidines/pharmacology , Pyrimidines/chemical synthesis
10.
Mar Drugs ; 22(6)2024 May 27.
Article in English | MEDLINE | ID: mdl-38921556

ABSTRACT

Tuberculosis, a persistent illness caused by Mycobacterium tuberculosis, remains a significant global public health challenge. The widespread use of anti-tuberculosis drugs has resulted in the emergence of drug-resistant strains, which complicates treatment efforts. Addressing this issue is crucial and hinges on the development of new drugs that can effectively target the disease. This involves identifying novel therapeutic targets that can disrupt the bacterium's survival mechanisms in various environments such as granulomas and lesions. Citrate lyase, essential for the survival of Mycobacterium species at lesion sites and in granulomatous conditions, is a potential target for the treatment of tuberculosis. This manuscript aimed to construct an efficient enzyme inhibitor screening platform using ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-QTOF MS). This system can accurately identify compounds with enzyme inhibitory activity from a library of marine terpenoids and phenolic compounds. Utilizing the screened herbal enzyme inhibitors as a starting point, we analyzed their chemical structures and skillfully built a library of marine compounds based on these structures. The results showed that all of the tested compounds from the phenolics library inhibited citrate lyase by more than 50%, and a significant portion of terpenoids also demonstrated inhibition, with these active terpenoids comprising over half of the terpenoids tested. The study underscores the potential of marine-derived phenolic and terpenoid compounds as potent inhibitors of citrate lyase, indicating a promising direction for future investigations in treating tuberculosis and associated disorders.


Subject(s)
Antitubercular Agents , Enzyme Inhibitors , Mycobacterium tuberculosis , Tandem Mass Spectrometry , Tandem Mass Spectrometry/methods , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Chromatography, High Pressure Liquid/methods , ATP Citrate (pro-S)-Lyase/antagonists & inhibitors , Aquatic Organisms , Terpenes/pharmacology , Terpenes/chemistry , Humans , Phenols/pharmacology , Phenols/chemistry , Chromatography, Liquid/methods
11.
Eur J Med Chem ; 274: 116559, 2024 Aug 05.
Article in English | MEDLINE | ID: mdl-38850856

ABSTRACT

Tuberculosis remains the second deadliest infectious disease in humans and a public health threat due to the emergence of multidrug-resistant (MDR-TB) and extensively drug-resistant (XDR-TB) strains. Therefore, it is urgent to identify new anti-tuberculosis treatments and novel therapeutic targets to prevent the emergence of resistance. In recent years, the study of anti-tuberculosis properties of nitroaromatic compounds has led to the identification of two novel biological targets, the deazaflavin (F420)-dependent nitroreductase Ddn and the decaprenylphosphoryl-ß-d-ribose 2'-epimerase DprE1. This review aims to show why Ddn and DprE1 are promising therapeutic targets and highlight nitroaromatic compounds interest in developing new anti-tuberculosis treatments active against MDR-TB and XDR-TB. Despite renewed interest in the development of new anti-tuberculosis nitroaromatic compounds, pharmaceutical companies often exclude nitro-containing molecules from their drug discovery programs because of their toxic and mutagenic potential. This exclusion results in missed opportunities to identify new nitroaromatic compounds and promising therapeutic targets.


Subject(s)
Antitubercular Agents , Mycobacterium tuberculosis , Nitroreductases , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Humans , Mycobacterium tuberculosis/drug effects , Nitroreductases/metabolism , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Nitro Compounds/chemistry , Nitro Compounds/pharmacology , Molecular Structure , Microbial Sensitivity Tests , Drug Development , Alcohol Oxidoreductases
12.
J Chem Inf Model ; 64(13): 5232-5241, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38874541

ABSTRACT

Discovered in the 1920s, cytochrome bd is a terminal oxidase that has received renewed attention as a drug target since its atomic structure was first determined in 2016. Only found in prokaryotes, we study it here as a drug target for Mycobacterium tuberculosis (Mtb). Most previous drug discovery efforts toward cytochrome bd have involved analogues of the canonical substrate quinone, known as Aurachin D. Here, we report six new cytochrome bd inhibitor scaffolds determined from a computational screen and confirmed on target activity through in vitro testing. These scaffolds provide new avenues for lead optimization toward Mtb therapeutics.


Subject(s)
Antitubercular Agents , Enzyme Inhibitors , Mycobacterium tuberculosis , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Enzyme Inhibitors/pharmacology , Enzyme Inhibitors/chemistry , Tuberculosis/drug therapy , Oxidoreductases/antagonists & inhibitors , Oxidoreductases/metabolism , Oxidoreductases/chemistry , Models, Molecular , Molecular Docking Simulation
13.
PLoS One ; 19(5): e0303173, 2024.
Article in English | MEDLINE | ID: mdl-38739587

ABSTRACT

In this study, new series of N'-(2-(substitutedphenoxy)acetyl)-4-(1H-pyrrol-1-yl)benzohydrazides (3a-j) 4-(2,5-dimethyl-1H-pyrrol-1-yl)-N'-(2-(substitutedphenoxy)acetyl)benzohydrazides (5a-j) were synthesized, characterized and assessed as inhibitors of enoyl ACP reductase and DHFR. Most of the compounds exhibited dual inhibition against the enzymes enoyl ACP reductase and DHFR. Several synthesized substances also demonstrated significant antibacterial and antitubercular properties. A molecular docking analysis was conducted in order to determine the potential mechanism of action of the synthesized compounds. The results indicated that there were binding interactions seen with the active sites of dihydrofolate reductase and enoyl ACP reductase. Additionally, important structural details were identified that play a critical role in sustaining the dual inhibitory activity. These findings were useful for the development of future dual inhibitors. Therefore, this study provided strong evidence that several synthesized molecules could exert their antitubercular properties at the cellular level through multi-target inhibition. By shedding light on the mechanisms through which these compounds exert their inhibitory effects, this research opens up promising avenues for the future development of dual inhibitors with enhanced antibacterial and antitubercular properties. The study's findings underscore the importance of multi-target approaches in drug design, providing a strong foundation for the design and optimization of novel compounds that can effectively target bacterial infections at the cellular level.


Subject(s)
Antitubercular Agents , Pyrroles , Tetrahydrofolate Dehydrogenase , Humans , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Antitubercular Agents/chemical synthesis , Catalytic Domain , Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/antagonists & inhibitors , Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism , Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/chemistry , Folic Acid Antagonists/pharmacology , Folic Acid Antagonists/chemistry , Folic Acid Antagonists/chemical synthesis , Microbial Sensitivity Tests , Molecular Docking Simulation , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/enzymology , Pyrroles/chemical synthesis , Pyrroles/chemistry , Pyrroles/pharmacology , Structure-Activity Relationship , Tetrahydrofolate Dehydrogenase/metabolism , Tetrahydrofolate Dehydrogenase/chemistry
14.
Int J Mol Sci ; 25(9)2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38732102

ABSTRACT

Cytochrome P450 CYP121A1 is a well-known drug target against Mycobacterium tuberculosis, the human pathogen that causes the deadly disease tuberculosis (TB). CYP121A1 is a unique P450 enzyme because it uses classical and non-classical P450 catalytic processes and has distinct structural features among P450s. However, a detailed investigation of CYP121A1 protein structures in terms of active site cavity dynamics and key amino acids interacting with bound ligands has yet to be undertaken. To address this research knowledge gap, 53 CYP121A1 crystal structures were investigated in this study. Critical amino acids required for CYP121A1's overall activity were identified and highlighted this enzyme's rigid architecture and substrate selectivity. The CYP121A1-fluconazole crystal structure revealed a novel azole drug-P450 binding mode in which azole heme coordination was facilitated by a water molecule. Fragment-based inhibitor approaches revealed that CYP121A1 can be inhibited by molecules that block the substrate channel or by directly interacting with the P450 heme. This study serves as a reference for the precise understanding of CYP121A1 interactions with different ligands and the structure-function analysis of P450 enzymes in general. Our findings provide critical information for the synthesis of more specific CYP121A1 inhibitors and their development as novel anti-TB drugs.


Subject(s)
Cytochrome P-450 Enzyme System , Mycobacterium tuberculosis , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Cytochrome P-450 Enzyme System/metabolism , Cytochrome P-450 Enzyme System/chemistry , Structure-Activity Relationship , Catalytic Domain , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/antagonists & inhibitors , Crystallography, X-Ray , Cytochrome P-450 Enzyme Inhibitors/pharmacology , Cytochrome P-450 Enzyme Inhibitors/chemistry , Models, Molecular , Humans , Protein Binding , Substrate Specificity , Ligands , Protein Conformation
15.
Chem Biodivers ; 21(6): e202400496, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38700369

ABSTRACT

Tuberculosis remains a global health threat, with increasing infection rates and mortality despite existing anti-TB drugs. The present work focuses on the research findings regarding the development and evaluation of thiadiazole-linked thiazole derivatives as potential anti-tuberculosis agents. We present the synthesis data and confirm the compound structures using spectroscopic techniques. The current study reports twelve thiazole-thiadiazole compounds (5 a-5 l) for their anti-tuberculosis and related bioactivities. This paper emphasizes compounds 5 g, 5 i, and 5 l, which exhibited promising MIC values, leading to further in silico and interaction analysis. Pharmacophore mapping data included in the present analysis identified tubercular ThyX as potential drug targets. The compounds were evaluated for anti-tubercular activity using standard methods, revealing significant MIC values, particularly compound 5 l, with the best MIC value of 7.1285 µg/ml. Compounds 5 g and 5 i also demonstrated moderate to good MIC values against M. tuberculosis (H37Ra). Structural inspection of the docked poses revealed interactions such as hydrogen bonds, halogen bonds, and interactions containing Pi electron cloud, shedding light on conserved interactions with residues like Arg 95, Cys 43, His 69, and Arg 87 from the tubercular ThyX enzyme.


Subject(s)
Antitubercular Agents , Microbial Sensitivity Tests , Molecular Docking Simulation , Mycobacterium tuberculosis , Thiadiazoles , Thiazoles , Antitubercular Agents/pharmacology , Antitubercular Agents/chemical synthesis , Antitubercular Agents/chemistry , Thiadiazoles/chemistry , Thiadiazoles/pharmacology , Thiadiazoles/chemical synthesis , Thiazoles/chemistry , Thiazoles/pharmacology , Thiazoles/chemical synthesis , Mycobacterium tuberculosis/drug effects , Structure-Activity Relationship , Molecular Structure , Humans
16.
ACS Infect Dis ; 10(6): 2288-2302, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38717380

ABSTRACT

The current tuberculosis (TB) treatment is challenged by a complex first-line treatment for drug-sensitive (DS) TB. Additionally, the prevalence of multidrug (MDR)- and extensively drug (XDR)-resistant TB necessitates the search for new drug prototypes. We synthesized and screened 30 hybrid compounds containing aminopyridine and 2-chloro-3-formyl quinoline to arrive at a compound with potent antimycobacterial activity, UH-NIP-16. Subsequently, antimycobacterial activity against DS and MDR Mycobacterium tuberculosis (M.tb) strains were performed. It demonstrated an MIC50 value of 1.86 ± 0.21 µM for laboratory pathogenic M.tb strain H37Rv and 3.045 ± 0.813 µM for a clinical M.tb strain CDC1551. UH-NIP-16 also decreased the MIC50 values of streptomycin, isoniazid, ethambutol, and bedaquiline to about 45, 55, 68, and 76%, respectively, when used in combination, potentiating their activities. The molecule was active against a clinical MDR M.tb strain. Cytotoxicity on PBMCs from healthy donors and on human cell lines was found to be negligible. Further, blind docking of UH-NIP-16 using Auto Dock Vina and MGL tools onto diverse M.tb proteins showed high binding affinities with multiple M.tb proteins, the top five targets being metabolically critical proteins CelA1, DevS, MmaA4, lysine acetyltransferase, and immunity factor for tuberculosis necrotizing toxin. These bindings were confirmed by fluorescence spectroscopy using a representative protein, MmaA4. Envisaging that a pathogen will have a lower probability of developing resistance to a hybrid molecule with multiple targets, we propose that UH-NIP-16 can be further developed as a lead molecule with the bacteriostatic potential against M.tb, both alone and in combination with first-line drugs.


Subject(s)
Antitubercular Agents , Isonicotinic Acids , Microbial Sensitivity Tests , Molecular Docking Simulation , Mycobacterium tuberculosis , Quinolines , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Antitubercular Agents/chemical synthesis , Antitubercular Agents/chemistry , Humans , Quinolines/pharmacology , Quinolines/chemistry , Quinolines/chemical synthesis , Isonicotinic Acids/pharmacology , Isonicotinic Acids/chemistry , Isonicotinic Acids/chemical synthesis , Tuberculosis/drug therapy , Tuberculosis/microbiology
17.
Comput Biol Med ; 176: 108573, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38723396

ABSTRACT

In this work we investigated the Pks13-TE domain, which plays a critical role in the viability of the mycobacteria. In this report, we have used a series of AI and Physics-based tools to identify Pks13-TE inhibitors. The Reinvent 4, pKCSM, KDeep, and SwissADME are AI-ML-based tools. AutoDock Vina, PLANTS, MDS, and MM-GBSA are physics-based methods. A combination of these methods yields powerful support in the drug discovery cycle. Known inhibitors of Pks13-TE were collected, curated, and used as input for the AI-based tools, and Mol2Mol molecular optimisation methods generated novel inhibitors. These ligands were filtered based on physics-based methods like molecular docking and molecular dynamics using multiple tools for consensus generation. Rigorous analysis was performed on the selected compounds to reduce the chemical space while retaining the most promising compounds. The molecule interactions, stability of the protein-ligand complexes and the comparable binding energies with the native ligand were essential factors for narrowing the ligands set. The filtered ligands from docking, MDS, and binding energy colocations were further tested for their ADMET properties since they are among the essential criteria for this series of molecules. It was found that ligands Mt1 to Mt6 have excellent predicted pharmacokinetic, pharmacodynamic and toxicity profiles and good synthesisability.


Subject(s)
Molecular Docking Simulation , Mycobacterium tuberculosis , Polyketide Synthases , Polyketide Synthases/metabolism , Polyketide Synthases/chemistry , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Bacterial Proteins/antagonists & inhibitors , Artificial Intelligence , Antitubercular Agents/chemistry , Antitubercular Agents/pharmacology , Antitubercular Agents/pharmacokinetics , Molecular Dynamics Simulation , Ligands , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Drug Discovery
18.
Sci Rep ; 14(1): 12170, 2024 05 28.
Article in English | MEDLINE | ID: mdl-38806590

ABSTRACT

Tuberculosis (TB) continues to be a global health crisis, necessitating urgent interventions to address drug resistance and improve treatment efficacy. In this study, we validate lumazine synthase (RibH), a vital enzyme in the riboflavin biosynthetic pathway, as a potential drug target against Mycobacterium tuberculosis (M. tb) using a CRISPRi-based conditional gene knockdown strategy. We employ a high-throughput molecular docking approach to screen ~ 600,000 compounds targeting RibH. Through in vitro screening of 55 shortlisted compounds, we discover 3 compounds that exhibit potent antimycobacterial activity. These compounds also reduce intracellular burden of M. tb during macrophage infection and prevent the resuscitation of the nutrient-starved persister bacteria. Moreover, these three compounds enhance the bactericidal effect of first-line anti-TB drugs, isoniazid and rifampicin. Corroborating with the in silico predicted high docking scores along with favourable ADME and toxicity profiles, all three compounds demonstrate binding affinity towards purified lumazine synthase enzyme in vitro, in addition these compounds exhibit riboflavin displacement in an in vitro assay with purified lumazine synthase indicative of specificity of these compounds to the active site. Further, treatment of M. tb with these compounds indicate reduced production of flavin adenine dinucleotide (FAD), the ultimate end product of the riboflavin biosynthetic pathway suggesting the action of these drugs on riboflavin biosynthesis. These compounds also show acceptable safety profile in mammalian cells, with a high selective index. Hence, our study validates RibH as an important drug target against M. tb and identifies potent antimycobacterial agents.


Subject(s)
Antitubercular Agents , Molecular Docking Simulation , Mycobacterium tuberculosis , Mycobacterium tuberculosis/enzymology , Mycobacterium tuberculosis/drug effects , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Multienzyme Complexes/antagonists & inhibitors , Multienzyme Complexes/metabolism , Drug Discovery , Bacterial Proteins/metabolism , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Humans , Tuberculosis/drug therapy , Tuberculosis/microbiology , Microbial Sensitivity Tests , Animals
19.
Bioorg Med Chem Lett ; 108: 129800, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38763480

ABSTRACT

In a quest to discover new antimalarial and antitubercular drugs, we have designed and synthesized a series of novel triazole-quinazolinone hybrids. The in vitro screening of the triazole-quinazolinone hybrid entities against the plasmodium species P. falciparum offered potent antimalarial molecules 6c, 6d, 6f, 6g, 6j & 6k owing comparable activity to the reference drugs. Furthermore, the target compounds were evaluated in vitro against Mycobacterium tuberculosis (MTB) H37Rv strain. Among the screened compounds, 6c, 6d and 6l were found to be the most active molecules with a MIC values of 19.57-40.68 µM. The cytotoxicity of the most active compounds was studied against RAW 264.7 cell line by MTT assay and no toxicity was observed. The computational study including drug likeness and ADMET profiling, DFT, and molecular docking study was done to explore the features of target molecules. The compounds 6a, 6g, and 6k exhibited highest binding affinity of -10.3 kcal/mol with docked molecular targets from M. tuberculosis. Molecular docking study indicates that all the molecules are binding to the falcipain 2 protease (PDB: 6SSZ) of the P. falciparum. Our findings indicated that these new triazole-quinazolinone hybrids may be considered hit molecules for further optimization studies.


Subject(s)
Antimalarials , Antitubercular Agents , Drug Design , Microbial Sensitivity Tests , Molecular Docking Simulation , Mycobacterium tuberculosis , Plasmodium falciparum , Quinazolinones , Triazoles , Antitubercular Agents/pharmacology , Antitubercular Agents/chemical synthesis , Antitubercular Agents/chemistry , Antimalarials/pharmacology , Antimalarials/chemical synthesis , Antimalarials/chemistry , Triazoles/chemistry , Triazoles/pharmacology , Triazoles/chemical synthesis , Mycobacterium tuberculosis/drug effects , Plasmodium falciparum/drug effects , Quinazolinones/chemistry , Quinazolinones/pharmacology , Quinazolinones/chemical synthesis , Mice , Structure-Activity Relationship , Animals , Molecular Structure , Dose-Response Relationship, Drug , RAW 264.7 Cells
20.
Molecules ; 29(9)2024 Apr 29.
Article in English | MEDLINE | ID: mdl-38731549

ABSTRACT

Targeting translation factor proteins holds promise for developing innovative anti-tuberculosis drugs. During protein translation, many factors cause ribosomes to stall at messenger RNA (mRNA). To maintain protein homeostasis, bacteria have evolved various ribosome rescue mechanisms, including the predominant trans-translation process, to release stalled ribosomes and remove aberrant mRNAs. The rescue systems require the participation of translation elongation factor proteins (EFs) and are essential for bacterial physiology and reproduction. However, they disappear during eukaryotic evolution, which makes the essential proteins and translation elongation factors promising antimicrobial drug targets. Here, we review the structural and molecular mechanisms of the translation elongation factors EF-Tu, EF-Ts, and EF-G, which play essential roles in the normal translation and ribosome rescue mechanisms of Mycobacterium tuberculosis (Mtb). We also briefly describe the structure-based, computer-assisted study of anti-tuberculosis drugs.


Subject(s)
Bacterial Proteins , Mycobacterium tuberculosis , Mycobacterium tuberculosis/metabolism , Mycobacterium tuberculosis/drug effects , Mycobacterium tuberculosis/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/chemistry , Protein Biosynthesis , Peptide Elongation Factors/metabolism , Peptide Elongation Factors/chemistry , Peptide Elongation Factors/genetics , Antitubercular Agents/pharmacology , Antitubercular Agents/chemistry , Ribosomes/metabolism , Models, Molecular , Tuberculosis/drug therapy , Tuberculosis/microbiology , Tuberculosis/metabolism , Protein Conformation
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