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ACS Omega Apr 2024Colorectal cancer (CRC) has witnessed a concerning increase in incidence and poses a significant therapeutic challenge due to its poor prognosis. There is a pressing...
Colorectal cancer (CRC) has witnessed a concerning increase in incidence and poses a significant therapeutic challenge due to its poor prognosis. There is a pressing demand to identify novel drug therapies to combat CRC. In this study, we addressed this need by utilizing the pharmacological profiles of anticancer drugs from the Genomics of Drug Sensitivity in Cancer (GDSC) database and developed QSAR models using the Support Vector Machine (SVM) algorithm for prediction of alternative and promiscuous anticancer compounds for CRC treatment. Our QSAR models demonstrated their robustness by achieving a high correlation of determination () after 10-fold cross-validation. For 12 CRC cell lines, ranged from 0.609 to 0.827. The highest performance was achieved for SW1417 and GP5d cell lines with values of 0.827 and 0.786, respectively. Further, we listed the most common chemical descriptors in the drug profiles of the CRC cell lines and we also further reported the correlation of these descriptors with drug activity. The KRFP314 fingerprint was the predominantly occurring descriptor, with the KRFPC314 fingerprint following closely in prevalence within the drug profiles of the CRC cell lines. Beyond predictive modeling, we also confirmed the applicability of our developed QSAR models via methods by conducting descriptor-drug analyses and recapitulating drug-to-oncogene relationships. We also identified two potential anti-CRC FDA-approved drugs, viomycin and diamorphine, using QSAR models. To ensure the easy accessibility and utility of our research findings, we have incorporated these models into a user-friendly prediction Web server named "ColoRecPred", available at https://project.iith.ac.in/cgntlab/colorecpred. We anticipate that this Web server can be used for screening of chemical libraries to identify potential anti-CRC drugs.
PubMed: 38680332
DOI: 10.1021/acsomega.4c01195 -
Frontiers in Chemistry 2024Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which... (Review)
Review
Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and -ketoglutarate to perform either C-hydroxylation, C-hydroxylation, C-hydroxylation, or C-C-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.
PubMed: 38406558
DOI: 10.3389/fchem.2024.1365494 -
Acta Crystallographica. Section F,... Jul 2023L-2,3-Diaminopropionic acid (L-Dap) is a nonproteinogenic amino acid that plays as an important role as a building block in the biosynthesis of several natural products,...
L-2,3-Diaminopropionic acid (L-Dap) is a nonproteinogenic amino acid that plays as an important role as a building block in the biosynthesis of several natural products, including capreomycin, viomycin, zwittermicin, staphyloferrin and dapdiamide. A previous study reported that CmnB and CmnK are two enzymes that are involved in the formation of L-Dap in the biosynthesis of capreomycin. CmnB catalyzes the condensation reaction of O-phospho-L-serine and L-glutamic acid to generate N-(1-amino-1-carboxyl-2-ethyl)glutamic acid, which subsequently undergoes oxidative hydrolysis via CmnK to generate the product L-Dap. Here, the crystal structure of CmnB in complex with the reaction intermediate PLP-α-aminoacrylate is reported at 2.2 Å resolution. Notably, CmnB is the second known example of a PLP-dependent enzyme that forms a monomeric structure in crystal packing. The crystal structure of CmnB also provides insights into the catalytic mechanism of the enzyme and supports the biosynthetic pathway of L-Dap reported in previous studies.
Topics: Amino Acids; Capreomycin; Crystallography, X-Ray; beta-Alanine; Glutamic Acid
PubMed: 37405487
DOI: 10.1107/S2053230X23005769 -
Archives of Microbiology Mar 2023Actinobacteria are the largest bacteria group with 18 significant lineages, which are ubiquitously distributed in all the possible terrains. They are known to produce...
Actinobacteria are the largest bacteria group with 18 significant lineages, which are ubiquitously distributed in all the possible terrains. They are known to produce more than 10,000 medically relevant compounds. Despite their ability to make critical secondary metabolites and genome sequences' availability, these two have not been linked with certainty. With this intent, our study aims at understanding the biosynthetic capacity in terms of secondary metabolite production in 528 Actinobacteria species from five different habitats, viz., soil, water, plants, animals, and humans. In our analysis of 9,646 clusters of 59 different classes, we have documented 64,000 SMs, of which more than 74% were of unique type, while 19% were partially conserved and 7% were conserved compounds. In the case of conserved compounds, we found the highest distribution in soil, 79.12%. We found alternate sources of antibiotics, such as viomycin, vancomycin, teicoplanin, fosfomycin, ficellomycin and patulin, and antitumour compounds, such as doxorubicin and tacrolimus in the soil. Also our study reported alternate sources for the toxin cyanobactin in water and plant isolates. We further analysed the clusters to determine their regulatory pathways and reported the prominent presence of the two component system of TetR/AcrR family, as well as other partial domains like CitB superfamily and HTH superfamily, and discussed their role in secondary metabolite production. This information will be helpful in exploring Actinobacteria from other environments and in discovering new chemical moieties of clinical significance.
Topics: Humans; Animals; Actinobacteria; Bacteria; Genome, Bacterial; Anti-Bacterial Agents; Secondary Metabolism; Multigene Family
PubMed: 36944761
DOI: 10.1007/s00203-023-03482-3 -
Frontiers in Microbiology 2022Resistance to tuberculosis (TB) drugs has become a major threat to global control efforts. Early case detection and drug susceptibility profiling of the infecting...
BACKGROUND
Resistance to tuberculosis (TB) drugs has become a major threat to global control efforts. Early case detection and drug susceptibility profiling of the infecting bacteria are essential for appropriate case management. The objective of this study was to determine the drug susceptibility profiles of difficult-to-treat (DTT) TB patients in Ghana.
METHODS
Sputum samples obtained from DTT-TB cases from health facilities across Ghana were processed for rapid diagnosis and detection of drug resistance using the Genotype MTBDR and Genotype MTBDR. from Hain Life science.
RESULTS
A total of 298 (90%) out of 331 sputum samples processed gave interpretable bands out of which 175 (58.7%) were resistant to at least one drug (ANY); 16.8% (50/298) were isoniazid-mono-resistant (INH), 16.8% (50/298) were rifampicin-mono-resistant (RIF), and 25.2% (75/298) were MDR. 24 (13.7%) of the ANY were additionally resistant to at least one second line drug: 7.4% (2 RIF, 1 INH, and 10 MDR samples) resistant to only FQs and 2.3% (2 RIF, 1 INH, and 1 MDR samples) resistant to AMG drugs kanamycin (KAN), amikacin (AMK), capreomycin (CAP), and viomycin (VIO). Additionally, there were 4.0% (5 RIF and 2 MDR samples) resistant to both FQs and AMGs. 81 (65.6%) out of 125 INH-resistant samples including INH and MDR had -mutations (MT) whereas 15 (12%) had -MT. The remaining 28 (22.4%) had both and MT. All the 19 FQ-resistant samples were mutants whereas the 10 AMGs were (3), (3) as well as , and co-mutants (4). Except for the seven pre-XDR samples, no sample had MT.
CONCLUSION
The detection of several pre-XDR TB cases in Ghana calls for intensified drug resistance surveillance and monitoring of TB patients to, respectively, ensure early diagnosis and treatment compliance.
PubMed: 36713197
DOI: 10.3389/fmicb.2022.1069292 -
American Journal of TherapeuticsAdvances in drug therapy for pulmonary tuberculosis have had an extraordinary impact on the incidence of tuberculosis in the United States in the past century, which has...
BACKGROUND
Advances in drug therapy for pulmonary tuberculosis have had an extraordinary impact on the incidence of tuberculosis in the United States in the past century, which has decreased from 113/100,000 persons in 1920 to 2.2/100,000 in 2020. Modern treatments have contributed to a remarkable decrease in hospitalizations and mortality and have had a significant impact on the duration and severity of illness, quality of life, and work potential of affected persons.
STUDY QUESTION
What are the milestones of the changes in the expert approach to the pharmacological management of pulmonary tuberculosis in the past century?
STUDY DESIGN
To determine the changes in the experts' approach to the management of pulmonary tuberculosis, as presented in a widely used textbook in the United States.
DATA SOURCES
The chapters describing the management of pulmonary tuberculosis in the 26 editions of Cecil Textbook of Medicine published from 1927 through 2020.
RESULTS
In the preantibiotic era (1927-1943), the Cecil authors emphasized rest, good food, and fresh air as the treatment pillars for pulmonary tuberculosis. The modern era (1947-1971) recorded the discovery of all the drugs that are still used for the initial treatment, in the following order: streptomycin, para-aminosalicylic acid, isoniazid, pyrazinamide, ethambutol, cycloserine, kanamycin, ethionamide, capreomycin, and rifampin. In the postmodern era (1975-2020), therapeutic advances continued with trials of many drug combinations aimed at ameliorating the duration of treatment, drug resistance adverse effects, and poor the recent addition of fluoroquinolones, bedaquiline, and clofazimine.
CONCLUSIONS
The pharmacological management of tuberculosis has remained archaic until the middle of the 20th century. Fundamental progress occurred in a very short period (1947-1971) and was because of the recognition of the antituberculous effect of many antibiotics and chemotherapy agents. The challenges created by mycobacterial infections resistant to multiple drugs remain and have prompted the addition of new drugs in the past decade.
Topics: Humans; Expert Testimony; Quality of Life; Aminosalicylic Acids; Drug Resistance; Drug Resistance, Microbial; Viomycin; Tuberculosis, Pulmonary; Tuberculosis; Streptomycin; Pyrazinamide; Isoniazid; Antitubercular Agents
PubMed: 36301538
DOI: 10.1097/MJT.0000000000001575 -
Frontiers in Chemistry 2022CmnC is an α-ketoglutarate (α-KG)-dependent non-heme iron oxygenase involved in the formation of the l-capreomycidine (l-Cap) moiety in capreomycin (CMN) biosynthesis....
Crystal structure of the α-ketoglutarate-dependent non-heme iron oxygenase CmnC in capreomycin biosynthesis and its engineering to catalyze hydroxylation of the substrate enantiomer.
CmnC is an α-ketoglutarate (α-KG)-dependent non-heme iron oxygenase involved in the formation of the l-capreomycidine (l-Cap) moiety in capreomycin (CMN) biosynthesis. CmnC and its homologues, VioC in viomycin (VIO) biosynthesis and OrfP in streptothricin (STT) biosynthesis, catalyze hydroxylation of l-Arg to form β-hydroxy l-Arg (CmnC and VioC) or β,γ-dihydroxy l-Arg (OrfP). In this study, a combination of biochemical characterization and structural determination was performed to understand the substrate binding environment and substrate specificity of CmnC. Interestingly, despite having a high conservation of the substrate binding environment among CmnC, VioC, and OrfP, only OrfP can hydroxylate the substrate enantiomer d-Arg. Superposition of the structures of CmnC, VioC, and OrfP revealed a similar folds and overall structures. The active site residues of CmnC, VioC, and OrfP are almost conserved; however Leu136, Ser138, and Asp249 around the substrate binding pocket in CmnC are replaced by Gln, Gly, and Tyr in OrfP, respectively. These residues may play important roles for the substrate binding. The mutagenesis analysis revealed that the triple mutant CmnC switches the substrate stereoselectivity from l-Arg to d-Arg with ∼6% relative activity. The crystal structure of CmnC in complex with d-Arg revealed that the substrate loses partial interactions and adopts a different orientation in the binding site. This study provides insights into the enzyme engineering to α-KG non-heme iron oxygenases for adjustment to the substrate stereoselectivity and development of biocatalysts.
PubMed: 36176888
DOI: 10.3389/fchem.2022.1001311 -
Tuberactinomycin antibiotics: Biosynthesis, anti-mycobacterial action, and mechanisms of resistance.Frontiers in Microbiology 2022The tuberactinomycins are a family of cyclic peptide ribosome-targeting antibiotics with a long history of use as essential second-line treatments for drug-resistant... (Review)
Review
The tuberactinomycins are a family of cyclic peptide ribosome-targeting antibiotics with a long history of use as essential second-line treatments for drug-resistant tuberculosis. Beginning with the identification of viomycin in the early 1950s, this mini-review briefly describes tuberactinomycin structures and biosynthesis, as well as their past and present application in the treatment of tuberculosis caused by infection with . More recent studies are also discussed that have revealed details of tuberactinomycin action on the ribosome as well as resistance mechanisms that have emerged since their introduction into the clinic. Finally, future applications of these drugs are considered in the context of their recent removal from the World Health Organization's List of Essential Medicines.
PubMed: 36033858
DOI: 10.3389/fmicb.2022.961921 -
Proceedings of the National Academy of... Apr 2022Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are...
Changes in bacterial ribosomal RNA (rRNA) methylation status can alter the activity of diverse groups of ribosome-targeting antibiotics. These modifications are typically incorporated by a single methyltransferase that acts on one nucleotide target and rRNA methylation directly prevents drug binding, thereby conferring drug resistance. Loss of intrinsic methylation can also result in antibiotic resistance. For example, Mycobacterium tuberculosis becomes sensitized to tuberactinomycin antibiotics, such as capreomycin and viomycin, due to the action of the intrinsic methyltransferase TlyA. TlyA is unique among antibiotic resistance-associated methyltransferases as it has dual 16S and 23S rRNA substrate specificity and can incorporate cytidine-2′-O-methylations within two structurally distinct contexts. Here, we report the structure of a mycobacterial 50S subunit-TlyA complex trapped in a postcatalytic state with a S-adenosyl-L-methionine analog using single-particle cryogenic electron microscopy. Together with complementary functional analyses, this structure reveals critical roles in 23S rRNA substrate recognition for conserved residues across an interaction surface that spans both TlyA domains. These interactions position the TlyA active site over the target nucleotide C2144, which is flipped from 23S Helix 69 in a process stabilized by stacking of TlyA residue Phe157 on the adjacent A2143. Base flipping may thus be a common strategy among rRNA methyltransferase enzymes, even in cases where the target site is accessible without such structural reorganization. Finally, functional studies with 30S subunit suggest that the same TlyA interaction surface is employed to recognize this second substrate, but with distinct dependencies on essential conserved residues.
Topics: Bacterial Proteins; Catalytic Domain; Drug Resistance, Bacterial; Methyltransferases; Mycobacterium tuberculosis; Protein Conformation, alpha-Helical; RNA, Ribosomal, 16S; RNA, Ribosomal, 23S; Ribosome Subunits, Large, Bacterial
PubMed: 35357969
DOI: 10.1073/pnas.2120352119 -
ACS Chemical Biology Jan 2022Capreomycin (CMN) is an important second-line antituberculosis antibiotic isolated from subspecies . The gene cluster for CMN biosynthesis has been identified and...
Capreomycin (CMN) is an important second-line antituberculosis antibiotic isolated from subspecies . The gene cluster for CMN biosynthesis has been identified and sequenced, wherein the gene was annotated as a phosphotransferase likely engaging in self-resistance. Previous studies reported that Cph inactivates two CMNs, CMN IA and IIA, by phosphorylation. We, herein, report that (1) harboring the gene becomes resistant to both CMN IIA and IIB, (2) phylogenetic analysis regroups Cph to a new clade in the phosphotransferase protein family, (3) Cph shares a three-dimensional structure akin to the aminoglycoside phosphotransferases with a high binding affinity () to both CMN IIA and IIB at micromolar levels, and (4) Cph utilizes either ATP or GTP as a phosphate group donor transferring its γ-phosphate to the hydroxyl group of CMN IIA. Until now, Cph and Vph (viomycin phosphotransferase) are the only two known enzymes inactivating peptide-based antibiotics through phosphorylation. Our biochemical characterization and structural determination conclude that Cph confers the gene-carrying species resistance to CMN by means of either chemical modification or physical sequestration, a naturally manifested belt and braces strategy. These findings add a new chapter into the self-resistance of bioactive natural products, which is often overlooked while designing new bioactive molecules.
Topics: Actinobacteria; Antibiotics, Antitubercular; Bacterial Proteins; Capreomycin; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Enzymologic; Models, Molecular; Molecular Structure; Phosphotransferases (Alcohol Group Acceptor); Phylogeny; Protein Conformation
PubMed: 34994196
DOI: 10.1021/acschembio.1c00799