An equation for biomimicking macromolecular crowding using Escherichia coli MG1655 strain

Khambhati, Khushal; Gohil, Nisarg; Bhattacharjee, Gargi; Panchasara, Happy; Singh, Vijai

doi:10.1016/j.bpc.2019.106244

Cited by 6 publications

(4 citation statements)

References 32 publications

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“…Each well was first filled with Mueller‐Hinton (MH) broth and various concentrations of synthesized naphthalene derivatives (1–1000 g/mL), and then each system was inoculated with a 10 % v/v standardized inoculum of test bacterial culture. The 0.5 McFarland turbidity standards were followed while developing the bacterial standardized inoculum in sterile saline (0.85 % NaCl) at OD600 [29,30] . Controls including sterility, growth, and positive control were also taken into account in addition to the various experimental concentrations.…”

Section: Methodsmentioning

confidence: 99%

“…The 0.5 McFarland turbidity standards were followed while developing the bacterial standardized inoculum in sterile saline (0.85 % NaCl) at OD600. [29,30] Controls including sterility, growth, and positive control were also taken into account in addition to the various experimental concentrations. Antibiotic chloramphenicol served as a positive control.…”

Section: Antibacterial Activitymentioning

confidence: 99%

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New Amino Acids Naphthalene Scaffolds as Potent Antimicrobial Agents: In Vitro Assay and In Silico Molecular Docking Study

Kalariya,

Pandya,

Gohil

et al. 2024

ChemistrySelect

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The development of innovative antifungal medications to address the issues of indiscriminate antifungal use contributes to certain antifungal drug resistance. To tackle this issue, we have designed and synthesized novel amino acids naphthalene scaffolds (6 a–6 i) (Scheme 1) by acid amine coupling between compound 5 and various amino acids. Moreover, we evaluated the antifungal, anti‐bacterial and antimalarial activities of synthesized derivatives. Among them, compounds Met (6 a), Phe (6 c), Lys (6 d), Ser (6 f), and Tyr (6 i) expressed excellent antifungal activity at a minimum inhibitory concentration (MIC) value of 250 μg/mL against Candida albicans compared to standard drug griseofulvin (500 μg/mL). The antibacterial assay results showed that compound Met (6 a) exhibited effective antibacterial activity at MIC value at 50 and 62.5 μg/mL against Streptococcus pyogenes and Pseudomonas aeruginosa respectively, and compound Trp (6 g) showed very good antibacterial activity at MIC 62.5 μg/mL against Staphylococcus aureus. The antimalarial activity of synthesized compoundsVal (6 b) and Lys (6 d) showed moderately active with mean IC50 of 0.69 and 0.47 μg/mL, respectively compared with standard drug quinine (IC50=0.26 μg/mL). Also, a molecular docking study was performed to demonstrate the binding energy of synthesized scaffoldswith effective interaction with various proteins. The compound Met (6 a) showed that the highest binding affinity (binding energy: −7.1 kcal/mol) which interacted more effectively with VAL 120 (2.90 Å).

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Section: Methodsmentioning

confidence: 99%

Section: Antibacterial Activitymentioning

confidence: 99%

New Amino Acids Naphthalene Scaffolds as Potent Antimicrobial Agents: In Vitro Assay and In Silico Molecular Docking Study

Kalariya,

Pandya,

Gohil

et al. 2024

ChemistrySelect

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“…All the complex media were purchased from HiMedia, India. Standardized microbial inoculum was prepared as per 0.5 McFarland turbidity standard at an optical density of 600 nm (OD 600 ) (Systronics Visiscan Spectrophotometer 167) using overnight grown C. violaceum colonies and adjusted with sterile normal saline solution (0.85% NaCl) (Gohil et al, 2020; Khambhati et al, 2019). The prepared inoculum (10% v/v) was then inoculated into sterile 100 mL Erlenmeyer flasks containing different sterile media and incubated at 37℃ for 48 hr in shaking condition (150 rpm).…”

Section: Methodsmentioning

confidence: 99%

Enhanced production of violacein by Chromobacterium violaceum using agro‐industrial waste soybean meal

Gohil

Bhattacharjee

Gayke

et al. 2021

J of Applied Microbiology

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Aims:The research is aimed at developing an economic and sustainable growth medium using abundantly available and highly nutritive agro-industrial waste soybean meal as the substrate for the production of violacein by Chromobacterium violaceum. Methods and Results:Violacein produced using soybean meal medium was compared with the commercial complex growth media. Upon utilization of 2% w/v soybean meal (SM 2 ) medium, 496 mg/L crude violacein was achieved after 48-hr incubation time, which was 1.62-fold higher than the crude violacein produced in Luria-Bertani (LB) broth. Additionally, supplementation of 100 mg/L L-tryptophan to 1% and 2% w/v soybean meal (SMT 1 and SMT 2 ) medium yielded 1217 mg/L (3.96fold higher as compared to LB) and 1198 mg/L (3.90-fold higher as compared to LB) crude violacein respectively. Optimization of culture conditions and concentration of L-tryptophan using Box-Behnken design (BBD) model produced as high as 1504.5 mg/L crude violacein. To the best of our knowledge, this is the highest crude violacein produced to date using agro-industrial-based waste as a substrate with minimal supplementation in a shake flask. Conclusions:The study signifies the potentiality of soybean meal as a cost-effective growth medium for the production of violacein. Optimization of the fermentation parameters clearly demonstrated a surge in violacein production. Significance and Impact of the Study: Utilization of soybean meal as an alternative to the expensive commercial media would surely promote the large-scale synthesis of this multifaceted compound.

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“…To mimic better physiology of cytoplasm, they examined the impact by altering the concentrations of magnesium and potassium, as well as by increasing molecular crowding with the addition of PEG 8000 (up to 4.5% wt/vol), which demonstrated dramatic effects on phage synthesis. To further explore the influence of macromolecular crowding in the CFPS system, an equation has been proposed to describe the in vitro biomimicry of the crowded environment present within E. coli in desire volume of reaction mixture using its lysate (Khambhati et al, 2019a). Sun et al (2013) have devised a novel method using E. coli BL21 Rosetta 2 strain, capable of accessing both the endogenous and exogenous cellular machinery of E. coli for protein synthesis.…”

Section: Preparation Of Cfps Systemsmentioning

confidence: 99%

Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems

Khambhati

Bhattacharjee

Gohil

et al. 2019

Front. Bioeng. Biotechnol.

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100

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Cell-free protein synthesis (CFPS) system is a simple, rapid, and sensitive tool that is devoid of membrane-bound barriers, yet contains all the mandatory substrates, biomolecules, and machineries required for the synthesis of the desired proteins. It has the potential to overcome loopholes in the current in vivo production systems and is a promising tool in both basic and applied scientific research. It facilitates a simplified organization of desired experiments with a variety of reaction conditions, making CFPS a powerful tool in biological research. It has been used for the expansion of genetic code, assembly of viruses, and in metabolic engineering for production of toxic and complex proteins. Subsequently, CFPS systems have emerged as potent technology for high-throughput production of membrane proteins, enzymes, and therapeutics. The present review highlights the recent advances and uses of CFPS systems in biomedical, therapeutic, and biotechnological applications. Additionally, we highlight possible solutions to the potential biosafety issues that may be encountered while using CFPS technology.

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An equation for biomimicking macromolecular crowding using Escherichia coli MG1655 strain

Cited by 6 publications

References 32 publications

New Amino Acids Naphthalene Scaffolds as Potent Antimicrobial Agents: In Vitro Assay and In Silico Molecular Docking Study

New Amino Acids Naphthalene Scaffolds as Potent Antimicrobial Agents: In Vitro Assay and In Silico Molecular Docking Study

Enhanced production of violacein by Chromobacterium violaceum using agro‐industrial waste soybean meal

Exploring the Potential of Cell-Free Protein Synthesis for Extending the Abilities of Biological Systems

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