Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation

Chakraborti, Sohini; Chakraborty, Moubani; Bose, Avipsa; Srinivasan, Narayanaswamy; Visweswariah, Sandhya S.

doi:10.3389/fmolb.2021.599221

Cited by 12 publications

(13 citation statements)

References 62 publications

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“…Further, using computational docking and library screening approaches, of the two natural compounds that could bind to MSMEG_3811(43), STOCKIN42384 (Figure 7A) had a docking score better than that of cAMP, and engaged Ala40 (a key residue for cAMP binding (10)) and Glu57 in hydrogen bonding. The second compound, STOCKIN74667 (Figure 7A), was hydrogen bonded to Gly114, also important for cAMP binding.…”

Section: Resultsmentioning

confidence: 99%

A universal stress protein is essential for the survival ofMycobacterium tuberculosis

Banerjee¹,

Chakraborty²,

Sharma³

et al. 2023

Preprint

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Mycobacterium tuberculosis employs several signaling pathways to regulate its cellular physiology and survival within the host. Mycobacterial genomes encode multiple adenylyl cyclases and cAMP effector proteins, underscoring the diverse ways in which these bacteria utilize cAMP. We have earlier identified universal stress proteins (USP), Rv1636 and MSMEG_3811 in M. tuberculosis and M. smegmatis respectively, as abundantly expressed, novel cAMP-binding proteins. In this study, we show that these USPs may function to regulate cAMP signaling by direct sequestration of the second messenger. In slow-growing mycobacteria, concentrations of Rv1636 were equivalent to the amounts of cAMP present in the cell, and overexpression of Rv1636 in M. smegmatis increased levels of 'bound' cAMP. Rv1636 is secreted via the SecA2 secretion system in M. tuberculosis but is not directly responsible for the efflux of cAMP from the cell. While msmeg_3811 could be readily deleted from the genome of M. smegmatis, we find that the rv1636 gene is essential for growth of M. tuberculosis, and this functionality depends on the cAMP-binding ability of Rv1636. This is the first evidence of a 'sink' for any second messenger in bacterial signaling that would allow mycobacterial cells to regulate the available intracellular 'free' pool of cAMP.

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Section: Resultsmentioning

confidence: 99%

A universal stress protein is essential for the survival ofMycobacterium tuberculosis

Banerjee¹,

Chakraborty²,

Sharma³

et al. 2023

Preprint

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“…Our other studies have shown that Rv1636 is a potential virulent protein that overexpresses host-derived stress conditions in response to mycobacterial infection. An in vitro experiment revealed that Rv1636 has a substantial binding affinity for ATP and cAMP [ 53 , 54 ]. As a result, we performed molecular docking of -Amyrin with Rv1636 using these two compounds as a control.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic Insight into the Enzymatic Inhibition of β-Amyrin against Mycobacterial Rv1636: In Silico and In Vitro Approaches

Beg

Sadaf

Shamsi

et al. 2022

Biology

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Mycobacterium tuberculosis has seen tremendous success as it has developed defenses to reside in host alveoli despite various host-related stress circumstances. Rv1636 is a universal stress protein contributing to mycobacterial survival in different host-derived stress conditions. Both ATP and cAMP can be bound with the Rv1636, and their binding actions are independent of one another. β-Amyrin, a triterpenoid compound, is abundant in medicinal plants and has many pharmacological properties and broad therapeutic potential. The current study uses biochemical, biophysical, and computational methods to define the binding of Rv1636 with β-Amyrin. A substantial interaction between β-Amyrin and Rv1636 was discovered by molecular docking studies, which helped decipher the critical residues involved in the binding process. VAL60 is a crucial residue found in the complexes of both Rv1636_β-Amyrin and Rv1636-ATP. Additionally, the Rv1636_β-Amyrin complex was shown to be stable by molecular dynamics simulation studies (MD), with minimal changes observed during the simulation. In silico observations were further complemented by in vitro assays. Successful cloning, expression, and purification of Rv1636 were accomplished using Ni-NTA affinity chromatography. The results of the ATPase activity assay indicated that Rv1636’s ATPase activity was inhibited in the presence of various β-Amyrin concentrations. Additionally, circular dichroism spectroscopy (CD) was used to examine modifications to Rv1636 secondary structure upon binding of β-Amyrin. Finally, isothermal titration calorimetry (ITC) advocated spontaneous binding of β-Amyrin with Rv1636 elucidating the thermodynamics of the Rv1636_β-Amyrin complex. Thus, the study establishes that β-Amyrin binds to Rv1636 with a significant affinity forming a stable complex and inhibiting its ATPase activity. The present study suggests that β-Amyrin might affect the functioning of Rv1636, which makes the bacterium vulnerable to different stress conditions.

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“…After sorting compounds based on the repetitive entries, 100 compounds were found unique and used for ligand preparation. 30 The structure of most of the compounds was downloaded from PubChem and ZINC databases, and the structures of other compounds were drawn using the chem-sketch Marvin visualization (https://chemaxon.com/products/marvin). All the compounds for this study were selected based on their respective mechanism toward the targeted receptors so that we can predict the best outcome for the particular disease pathway.…”

Section: Library Preparationmentioning

confidence: 99%

“…For the virtual screening process, all the libraries were subjected to the pdbqt format of receptor protein. 30 Furthermore, all the compounds were subjected to pharmacological screening, such as ADME and toxicity, followed by the Lipinski rule of five.…”

Section: Library Preparationmentioning

confidence: 99%

Computational Studies to Identify Potential Inhibitors Targeting the DprE1 Protein in Mycobacterium tuberculosis

Sheikh

Rizvi

et al. 2022

Int J. Pharm. Investigation

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Background: DprE1, which is a flavoenzyme, is very important for cell wall biosynthesis in Mycobacterium tuberculosis (Mtb) and for the pathogenesis, virulence, lethality, and stress resistance of the host. Drug-resistant tuberculosis is a challenging global human health issue, necessitating the development of novel, more effective treatment regimens without adverse effects. DprE1 represents a potential therapeutic target. It was explored as a drug target utilizing benzothiazoles (BTZ), which are enormously potential anti-bacterial agents and are currently being explored as anti-mycobacterial entities. Materials and Methods: We used virtual screening of bioactive molecules from PubChem and ZINC databases targeting DprE1, having bioactive thousands of molecules known for anti-microbial activity. In the present study, we selected 100 compounds as the most promising candidates to act as potential DprE1 inhibitors to control this emerging condition of tuberculosis infection. To identify the six topranked compounds, molecular docking was used to calculate the binding affinities (ranging from -8.3 to 10.0 kcal/mol) between various compounds (C1-C6) and the DprE1 protein.Results: Based on the results of an ADMET analysis, these six chemicals are safer potential drug candidates, as neither AMES toxicity nor carcinogenicity is present when toxicological properties are considered. Out of 6 compounds, the top-ranked compound exhibiting the best binding affinity against the drug target DprE1 (Pdb-id;4FEH) receptor was further subjected to molecular dynamic simulation for 100 nanoseconds to check the stability and trajectories by root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) graphs and interacting coordinates using Desmond Schrodinger Software. Conclusion: Our in-silico investigation identified potent inhibitors for the DprE1 protein of Mtb, and these compounds can be considered and recommended as the lead molecules in the treatment of tuberculosis.

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Identification of Potential Binders of Mtb Universal Stress Protein (Rv1636) Through an in silico Approach and Insights Into Compound Selection for Experimental Validation

Cited by 12 publications

References 62 publications

A universal stress protein is essential for the survival ofMycobacterium tuberculosis

A universal stress protein is essential for the survival ofMycobacterium tuberculosis

Mechanistic Insight into the Enzymatic Inhibition of β-Amyrin against Mycobacterial Rv1636: In Silico and In Vitro Approaches

Computational Studies to Identify Potential Inhibitors Targeting the DprE1 Protein in Mycobacterium tuberculosis

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