scholarly journals Evaluation of Different Mycobacterial Species for Drug Discovery and Characterisation of Novel Inhibitors of Mycobacterium Tuberculosis

2021 ◽  
Author(s):  
◽  
Mudassar Altaf
Keyword(s):  
Drug Discovery ◽  
Rnase H ◽  
Tuberculosis H37rv ◽  
Comparative Genomic ◽  
Tb Treatment ◽  
Compound Libraries ◽  
Genomic Study ◽  
Rnase Hi ◽  
Anti Hiv

<p>Tuberculosis (Tb) has plagued mankind for many centuries and is still a leading cause of death worldwide. A worrying development is the emergence of drug-resistant Tb that poses further challenges to the control of the disease. The global Tb burden and high mortality rate indicate that new drugs are needed for Tb treatment. While no new anti-Tb agents have been introduced to the market for about three decades, drugs with novel mechanisms of action can amend the current Tb treatment regimen and may provide an effective solution to drug resistance. The main objectives of this study were to identify an appropriate in vitro model that could be used for anti-Tb drug high-throughput screening (HTS), and to use this model to identify a novel candidate anti-tubercular drug and its cognate cellular target. A sensitive growth inhibition assay was set up with a GFP-labelled Tb vaccine strain, M. bovis BCG, using standard first and second line anti-tubercular drugs. HTS of the drug libraries was performed with various in vitro models to evaluate their efficacy for use in anti-Tb drug discovery. Approximately 50% of the M. tuberculosis inhibitors were not detected in screening with the surrogate species, M. smegmatis; whereas, only 21% of hits were not detected with M. bovis BCG. A comparative genomic study revealed that 97% of M. bovis BCG proteins, compared to 70% in M. smegmatis have conserved orthologues in M. tuberculosis H37Rv. Therefore, M. bovis BCG represented a more sensitive model than M. smegmatis for detecting anti-M. tuberculosis compounds. M. bovis BCG was then used to screen for novel anti-Tb agents by HTS of compound libraries and various plant extracts, followed by validation of new compounds in M. tuberculosis H37Ra. A number of novel M. tuberculosis inhibitors were identified, including sappanone A dimethyl ether from plant sources and compounds NSC112200 and NSC402959 from NIH chemical libraries. The inhibitors that were validated using M. tuberculosis H37Ra were also validated in the virulent Tb strain, M. tuberculosis H37Rv. In addition, their activity was further investigated using a suite of other clinically important human pathogens. One of the key anti-mycobacterial hits identified in this study, NSC402959, has previously been detected in screens for compounds that inhibit ribonuclease H (RNase H), an enzyme that is required for a number of essential cellular processes. NSC402959 inhibited RNase H proteins from HIV as well as from E. coli. Since HIV and Tb are major pandemics, previously-known anti-HIV RNase H compounds were imported and tested for their anti-proliferative activity towards M. tuberculosis H37Ra. HIV RNase H inhibitors, NSC35676, NSC112200, NSC133457 and NSC668394, exhibited good anti-mycobacterial activity in this study. In silico analysis suggested a plausible interaction of these inhibitors with mycobacterial RNase HI. A biochemical assay further confirmed NSC112200 to be specific against RNase HI from M. tuberculosis. These interesting inhibitors were not only structurally different from existing anti-Tb drugs but some of them were also non-toxic to mammalian cells and may have a unique mechanism of action. Thus, these compounds showed good potential for development as dual inhibitors of Tb and HIV; therefore, future studies in animal infection models to determine their dual anti-mycobacterial and anti-HIV activities are warranted.</p>

scholarly journals Evaluation of Different Mycobacterial Species for Drug Discovery and Characterisation of Novel Inhibitors of Mycobacterium Tuberculosis

2021 ◽  
Author(s):  
◽  
Mudassar Altaf
Keyword(s):  
Drug Discovery ◽  
Rnase H ◽  
Tuberculosis H37rv ◽  
Comparative Genomic ◽  
Tb Treatment ◽  
Compound Libraries ◽  
Genomic Study ◽  
Rnase Hi ◽  
Anti Hiv

<p>Tuberculosis (Tb) has plagued mankind for many centuries and is still a leading cause of death worldwide. A worrying development is the emergence of drug-resistant Tb that poses further challenges to the control of the disease. The global Tb burden and high mortality rate indicate that new drugs are needed for Tb treatment. While no new anti-Tb agents have been introduced to the market for about three decades, drugs with novel mechanisms of action can amend the current Tb treatment regimen and may provide an effective solution to drug resistance. The main objectives of this study were to identify an appropriate in vitro model that could be used for anti-Tb drug high-throughput screening (HTS), and to use this model to identify a novel candidate anti-tubercular drug and its cognate cellular target. A sensitive growth inhibition assay was set up with a GFP-labelled Tb vaccine strain, M. bovis BCG, using standard first and second line anti-tubercular drugs. HTS of the drug libraries was performed with various in vitro models to evaluate their efficacy for use in anti-Tb drug discovery. Approximately 50% of the M. tuberculosis inhibitors were not detected in screening with the surrogate species, M. smegmatis; whereas, only 21% of hits were not detected with M. bovis BCG. A comparative genomic study revealed that 97% of M. bovis BCG proteins, compared to 70% in M. smegmatis have conserved orthologues in M. tuberculosis H37Rv. Therefore, M. bovis BCG represented a more sensitive model than M. smegmatis for detecting anti-M. tuberculosis compounds. M. bovis BCG was then used to screen for novel anti-Tb agents by HTS of compound libraries and various plant extracts, followed by validation of new compounds in M. tuberculosis H37Ra. A number of novel M. tuberculosis inhibitors were identified, including sappanone A dimethyl ether from plant sources and compounds NSC112200 and NSC402959 from NIH chemical libraries. The inhibitors that were validated using M. tuberculosis H37Ra were also validated in the virulent Tb strain, M. tuberculosis H37Rv. In addition, their activity was further investigated using a suite of other clinically important human pathogens. One of the key anti-mycobacterial hits identified in this study, NSC402959, has previously been detected in screens for compounds that inhibit ribonuclease H (RNase H), an enzyme that is required for a number of essential cellular processes. NSC402959 inhibited RNase H proteins from HIV as well as from E. coli. Since HIV and Tb are major pandemics, previously-known anti-HIV RNase H compounds were imported and tested for their anti-proliferative activity towards M. tuberculosis H37Ra. HIV RNase H inhibitors, NSC35676, NSC112200, NSC133457 and NSC668394, exhibited good anti-mycobacterial activity in this study. In silico analysis suggested a plausible interaction of these inhibitors with mycobacterial RNase HI. A biochemical assay further confirmed NSC112200 to be specific against RNase HI from M. tuberculosis. These interesting inhibitors were not only structurally different from existing anti-Tb drugs but some of them were also non-toxic to mammalian cells and may have a unique mechanism of action. Thus, these compounds showed good potential for development as dual inhibitors of Tb and HIV; therefore, future studies in animal infection models to determine their dual anti-mycobacterial and anti-HIV activities are warranted.</p>

Current Approaches to Drug Discovery for Chagas Disease: Methodological Advances

2019 ◽  
Vol 22 (8) ◽  
pp. 509-520
Author(s):  
Cauê B. Scarim ◽  
Chung M. Chin
Keyword(s):  
Drug Discovery ◽  
Chagas Disease ◽  
Drug Candidates ◽  
Lead Compounds ◽  
New Drug ◽  
Compound Libraries ◽  
Screening Assays ◽  
Cruzi Infection

Background: In recent years, there has been an improvement in the in vitro and in vivo methodology for the screening of anti-chagasic compounds. Millions of compounds can now have their activity evaluated (in large compound libraries) by means of high throughput in vitro screening assays. Objective: Current approaches to drug discovery for Chagas disease. Method: This review article examines the contribution of these methodological advances in medicinal chemistry in the last four years, focusing on Trypanosoma cruzi infection, obtained from the PubMed, Web of Science, and Scopus databases. Results: Here, we have shown that the promise is increasing each year for more lead compounds for the development of a new drug against Chagas disease. Conclusion: There is increased optimism among those working with the objective to find new drug candidates for optimal treatments against Chagas disease.

scholarly journals A Comparative Genomic Study of Attenuated and Virulent Strains of Babesia bigemina

Pathogens ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 318
Author(s):  
Bernardo Sachman-Ruiz ◽  
Luis Lozano ◽  
José J. Lira ◽  
Grecia Martínez ◽  
Carmen Rojas ◽  
...  
Keyword(s):  
In Vitro Culture ◽  
Virulence Genes ◽  
Laboratory Strain ◽  
Host Cells ◽  
Comparative Genomic ◽  
Local Alignment ◽  
Host Immune System ◽  
Babesia Bigemina ◽  
Genomic Study

Cattle babesiosis is a socio-economically important tick-borne disease caused by Apicomplexa protozoa of the genus Babesia that are obligate intraerythrocytic parasites. The pathogenicity of Babesia parasites for cattle is determined by the interaction with the host immune system and the presence of the parasite’s virulence genes. A Babesia bigemina strain that has been maintained under a microaerophilic stationary phase in in vitro culture conditions for several years in the laboratory lost virulence for the bovine host and the capacity for being transmitted by the tick vector. In this study, we compared the virulome of the in vitro culture attenuated Babesia bigemina strain (S) and the virulent tick transmitted parental Mexican B. bigemina strain (M). Preliminary results obtained by using the Basic Local Alignment Search Tool (BLAST) showed that out of 27 virulence genes described and analyzed in the B. bigemina virulent tick transmitted strain, only five were fully identified in the attenuated laboratory strain. In all cases, the identity and coverture of the identified genes of the wildtype strain were higher than those of the laboratory strain. This finding is putatively associated with the continuous partial loss of virulence genes in the laboratory strain after several passages of the parasite population under optimal in vitro growth conditions. The loss of virulence factors might be reflected in the absence of symptoms of the disease in cattle inoculated with the attenuated strain despite the presence of infection in the bovine host cells.

A Generally Applicable, High-Throughput Screening–Compatible Assay to Identify, Evaluate, and Optimize Antimicrobial Agents for Drug Therapy

2004 ◽  
Vol 9 (7) ◽  
pp. 578-587 ◽  
Author(s):  
Gerald Kleymann ◽  
Hans-Otto Werling
Keyword(s):  
Drug Discovery ◽  
High Throughput Screening ◽  
Antimicrobial Agents ◽  
Natural Infection ◽  
Test System ◽  
Test Method ◽  
Host Cells ◽  
Lethal Challenge ◽  
Compound Libraries

Efficacy and tolerability are the key criteria for a successful medication in the clinic. Therefore, a new test method to obtain selective and active lead molecules has been developed. Recently, this novel screening strategy enabled a breakthrough in drug discovery in the field of herpes viruses. Here the authors report that this assay is a generally applicable screening test, which allows not only for identifying tolerable and potent antimicrobial agents in compound libraries, but also covers all potential in vitro targets of both the pathogen and the host simultaneously. The test system mimics the smallest unit of a natural infection. Host cells are incubated in the presence of the test sample and are infected with microbes, such as viruses, bacteria, or fungi. Analogous to (lethal challenge) animal models, cell survival is determined. This assay maximizes the chances of success of anti-infective drug discovery, is sensitive, robust, time- and cost-efficient, and especially effective in optimizing screening hits to lead structures and development candidates. In addition to the minimal inhibitory concentration or dose, this test system simultaneously provides the selectivity index, a measure of tolerability in vitro. The authors propose the activity selectivity assay format as a new standard in anti-infective drug discovery and clinical development.

scholarly journals In Vitro Anti-HIV-1 Reverse Transcriptase and Integrase Properties of Punica granatum L. Leaves, Bark, and Peel Extracts and Their Main Compounds

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2124
Author(s):  
Cinzia Sanna ◽  
Arianna Marengo ◽  
Stefano Acquadro ◽  
Alessia Caredda ◽  
Roberta Lai ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Ellagic Acid ◽  
Punica Granatum ◽  
Rnase H ◽  
Hydrolyzable Tannins ◽  
Ic50 Values ◽  
Anti Hiv ◽  
Punica Granatum L ◽  
Hiv 1

In a search for natural compounds with anti-HIV-1 activity, we studied the effect of the ethanolic extract obtained from leaves, bark, and peels of Punica granatum L. for the inhibition of the HIV-1 reverse transcriptase (RT)-associated ribonuclease H (RNase H) and integrase (IN) LEDGF-dependent activities. The chemical analyses led to the detection of compounds belonging mainly to the phenolic and flavonoid chemical classes. Ellagic acid, flavones, and triterpenoid molecules were identified in leaves. The bark and peels were characterized by the presence of hydrolyzable tannins, such as punicalins and punicalagins, together with ellagic acid. Among the isolated compounds, the hydrolyzable tannins and ellagic acid showed a very high inhibition (IC50 values ranging from 0.12 to 1.4 µM and 0.065 to 0.09 µM of the RNase H and IN activities, respectively). Of the flavonoids, luteolin and apigenin were found to be able to inhibit RNase H and IN functions (IC50 values in the 3.7–22 μM range), whereas luteolin 7-O-glucoside showed selective activity for HIV-1 IN. In contrast, betulinic acid, ursolic acid, and oleanolic acid were selective for the HIV-1 RNase H activity. Our results strongly support the potential of non-edible P. granatum organs as a valuable source of anti-HIV-1 compounds.

scholarly journals Inactivation of thymidine kinase as a cause of resistance to zidovudine in clinical isolates of Escherichia coli: a phenotypic and genomic study

2020 ◽  
Vol 75 (6) ◽  
pp. 1410-1414
Author(s):  
Lucie Peyclit ◽  
Maryem Ben Khedher ◽  
Lotfi Zerrouki ◽  
Seydina M Diene ◽  
Sophie Alexandra Baron ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Thymidine Kinase ◽  
Gene Sequence ◽  
Stop Codon ◽  
Genomic Analysis ◽  
Clinical Isolates ◽  
Comparative Genomic ◽  
E Coli ◽  
Genomic Study

Abstract Objectives The antiviral zidovudine has been recently identified as an active drug against resistant Enterobacteriaceae, but prevalence of resistance to this compound remains unknown. The aim was to estimate the prevalence of clinical Escherichia coli isolates resistant to zidovudine and to decipher the mechanism of zidovudine resistance. Methods We screened 537 isolates on zidovudine-containing agar plates and studied their thymidine kinase (tdk) gene sequences, the putative target involved in zidovudine resistance. Moreover, sequence analysis of 633 complete genomes of E. coli was performed to investigate mutation in the tdk gene. A comparative genomic analysis was done on an in vitro zidovudine-resistant mutant. Results After screening on our medium containing 2.7 mg/L (10 μM) zidovudine, nine strains had a zidovudine MIC &gt;26.7 mg/L. The gene was absent in three isolates, inactivated by an IS (IS1X2 and ISApl1) in two isolates and mutated in four isolates. A genomic analysis of 633 E. coli genomes showed heterogeneity of the tdk gene sequence, with 27 different sequences. Among them, three genomes showed an inactivation of the gene (IS, stop codon and no tdk gene sequence). The in vitro mutant E. coli had 27 SNPs in eight genes of the core genome compared with the initial strain. Conclusions Our study reports zidovudine-resistant clinical isolates of E. coli, presumably related to tdk inactivation. Diversity of Tdk in bacterial genomes can be large. Other mechanisms need to be considered in zidovudine resistance. The use of zidovudine in antibiotic-resistant infections needs to be in combination and should be tested before clinical administration.

scholarly journals Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA–DNA junction

2004 ◽  
Vol 381 (3) ◽  
pp. 795-802 ◽  
Author(s):  
Naoto OHTANI ◽  
Hiroshi YANAGAWA ◽  
Masaru TOMITA ◽  
Mitsuhiro ITAYA
Keyword(s):  
Amino Acid ◽  
Rnase H ◽  
Single Type ◽  
Growth Defect ◽  
Okazaki Fragment ◽  
E Coli ◽  
H Gene ◽  
Rnase Hi

All the archaeal genomes sequenced to date contain a single Type 2 RNase H gene. We found that the genome of a halophilic archaeon, Halobacterium sp. NRC-1, contains an open reading frame with similarity to Type 1 RNase H. The protein encoded by the Vng0255c gene, possessed amino acid sequence identities of 33% with Escherichia coli RNase HI and 34% with a Bacillus subtilis RNase HI homologue. The B. subtilis RNase HI homologue, however, lacks amino acid sequences corresponding to a basic protrusion region of the E. coli RNase HI, and the Vng0255c has the similar deletion. As this deletion apparently conferred a complete loss of RNase H activity on the B. subtilis RNase HI homologue protein, the Vng0255c product was expected to exhibit no RNase H activity. However, the purified recombinant Vng0255c protein specifically cleaved an RNA strand of the RNA/DNA hybrid in vitro, and when the Vng0255c gene was expressed in an E. coli strain MIC2067 it could suppress the temperature-sensitive growth defect associated with the loss of RNase H enzymes of this strain. These results in vitro and in vivo strongly indicate that the Halobacterium Vng0255c is the first archaeal Type 1 RNase H. This enzyme, unlike other Type 1 RNases H, was able to cleave an Okazaki fragment-like substrate at the junction between the 3′-side of ribonucleotide and 5′-side of deoxyribonucleotide. It is likely that the archaeal Type 1 RNase H plays a role in the removal of the last ribonucleotide of the RNA primer from the Okazaki fragment during DNA replication.

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