Detailed investigation of catalytically important residues of class A ß-lactamase.

An increasing global health challenge is antimicrobial resistance. Bacterial infections are often treated by using ß-lactam antibiotics. But several resistance mechanisms have evolved in clinically mutated bacteria, which results in resistance against such antibiotics. Among which production of novel ß-lactamase is the major one. This results in bacterial resistance against penicillin, cephalosporin, and carbapenems, which are considered to be the last resort of antibacterial treatment. Hence, ß-lactamase enzymes produced by such bacteria are called extended-spectrum ß-lactamase and carbapenemase enzymes. Further, these bacteria have developed resistance against many ß-lactamase inhibitors as well. So, investigation of important residues that play an important role in altering and expanding the spectrum activity of these ß-lactamase enzymes becomes necessary. This review aims to gather knowledge about the role of residues and their mutations in class A ß-lactamase, which could be responsible for ß-lactamase mediated resistance. Class A ß-lactamase enzymes contain most of the clinically significant and expanded spectrum of ß-lactamase enzymes. Ser70, Lys73, Ser130, Glu166, and Asn170 residues are mostly conserved and have a role in the enzyme's catalytic activity. In-depth investigation of 69, 130, 131, 132, 164, 165, 166, 170, 171, 173, 176, 178, 179, 182, 237, 244, 275 and 276 residues were done along with its kinetic analysis for knowing its significance. Further, detailed information from many previous studies was gathered to know the effect of mutations on the kinetic activity of class A ß-lactamase enzymes with ß-lactam antibiotics.Communicated by Ramaswamy H. Sarma.

Insights into structure and activity relationship of clinically mutated PER1 and PER2 class A ß-lactamase enzymes.

PER1 and PER2 are among the class A ß-lactamase enzymes, which have evolved clinically to form antibiotic resistance and have significantly expanded their spectrum of activity. Hence, there is a need to study the clinical mutation responsible for such ß-lactamase mediated antibiotic resistance. Alterations in catalytic centre and Ω-loop structure could be the cause of antibiotic resistance in these ß-lactamase enzymes. Structural and functional alterations are caused due to mutations on or near the catalytic centre, which results in active site plasticity and are responsible for its expanded spectrum of activity in these class A ß-lactamase enzymes. Multiple sequence alignment, structure, kinetic, molecular docking, MMGBSA and molecular dynamic simulation comparisons were done on 38 clinically mutated and wild class A ß-lactamase enzymes. This work shows that PER1 and PER2 enzymes contains most unique mutations and have altered Ω-loop structure, which could be responsible for altering the structure-activity relationship and extending the spectrum of activity of these enzymes. Alterations in molecular docking, MMGBSA, kinetic values reveals the modification in the binding and activity of these clinically mutated enzymes with antibiotics. Further, the cause of these alterations can be revealed by active site interactions and H-bonding pattern of these enzymes with antibiotics. Met69Gln, Glu104Thr, Tyr105Trp, Met129His, Pro167Ala, Glu168Gln, Asn170His, Ile173Asp and Asp176Gln mutations were uniquely found in PER1 and PER2 enzymes. These mutations occurs at catalytic important residues and results in altered interactions with ß-lactam antibiotics. Hence, these mutations could be responsible for altering the structure-activity of PER1 and PER2 enzymes.Communicated by Ramaswamy H. Sarma.

An Extensive Review on ß-lactamase Enzymes and their Inhibitors.

ß-lactam antibiotics treat bacterial infections very effectively, but overuse and misuse have led to resistance. ß-lactamase enzymes hydrolyze ß-lactam antibiotics and are the primary cause of resistance in bacteria. Bacteria evolve and clinically mutate to produce such ß -lactamase enzymes, which could hydrolyze newly discovered antibiotics. Therefore, carbapenems are considered to be the last resort for antimicrobial treatment. Further, different inhibitors have been discovered to fight these evolving and mutating ß- lactamase enzyme resistance. These inhibitors are given in combination with the ß-lactam antibiotics to treat bacterial infections effectively. But in due course of time, it has been observed that bacteria develop resistance against this combination. This is an extensive review that discusses different classes of ß-lactamase enzymes, their mechanism of action, and the role of critical structural elements like loops and catalytically relevant mutations. Such mutations and structural modifications result in expanding the spectrum of activity, making these ß-lactamase enzymes resistant to the newly discovered ß-lactam antibiotics and their inhibitors. Detailed knowledge of such mutations, catalytically relevant structural modifications, related kinetics, and action mechanisms could help develop new inhibitors effectively. Further, a detailed discussion of available inhibitors against each class of ß-lactamase enzymes is also present.

WITHDRAWN: In-Silico Study of Resveratrol as Multi-Edged Potent Inhibitor against SARSCov- 2 and Variants of Concern Using Molecular Dynamic Simulation and PCA Analysis

The article has been withdrawn at the request of the author.Bentham Science apologizes to the readers of the journal for any inconvenience this may have caused.The Bentham Editorial Policy on Article Withdrawal can be found at https://benthamscience.com/editorial-policies-main.php. Bentham Science Disclaimer: It is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere. Furthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained. Plagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered. By submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.

Mutations responsible for the carbapenemase activity of SME-1.

SME-1 is a carbapenemase, produced by Serratia marcescens organism and causes nosocomial infections such as in bloodstream, wounds, urinary tract, or respiratory tract infections. Treatment of such infections becomes very complex due its resistance towards penicillins, cephalosporins, monobactams, and carbapenems. Resistance to such antibiotics is of great medical concern. The misuse and overuse of these antibiotics result in the clinical mutation and production of novel ß-lactamase enzymes such as SME-1, which show resistance to carbapenems. Class A contains most of the clinically significant extended spectrum of ß-lactamase enzymes and carbapenemases. In this study, class A ß-lactamase SME-1 sequence, structure, and binding were compared with naturally mutated class A ß-lactamase enzymes and a wild-type TEM-1. This study was performed for revealing mutations, which could be responsible for the carbapenemase activity of SME-1. The dynamic characteristics of SME-1 enzymes manifest a different degree of conservation and variability, which confers them to possess carbapenemase activities. Met69Cys, Glu104Tyr, Tyr105His, Ala237Ser, and Gly238Cys mutations occur in SME-1 as compared to wild-type TEM-1. These mutated residues are present close to active site residues such as Ser70, Lys73, Ser130, Asn132, Glu166, and Asn170, which participate in the hydrolytic reaction of ß-lactam antibiotics. Furthermore, these mutated residues demonstrate altered interactions with the ß-lactam antibiotics (results in altered binding) and within themselves (results in active site structure alterations), which results in expanding the spectrum of activity of these enzymes. This study provides important insights into the structure and activity relationship of SME-1 enzymes. This is evident from the Ω-loop structure modification, which forms the wall of the active site and repositioning of residues involved in hydrolytic reactions, when present in the complex with meropenem in a stable state of MD simulation at 50 ns. Hence, Met69Cys, Glu104Tyr, Tyr105His, Ala237Ser, and Gly238Cys mutations could result in an altered active site structure, binding, and activity of SME-1 with meropenem and thus become resistantant against meropenem, which is a carbapenem.

Prediction of suitable T and B cell epitopes for eliciting immunogenic response against SARS-CoV-2 and its mutant.

Spike glycoprotein of SARS-CoV-2 is mainly responsible for the recognition and membrane fusion within the host and this protein has an ability to mutate. Hence, T cell and B cell epitopes were derived from the spike glycoprotein sequence of wild SARS-CoV-2. The proposed T cell and B cell epitopes were found to be antigenic and conserved in the sequence of SARS-CoV-2 mutant (B.1.1.7). Thus, the proposed epitopes are effective against SARS-CoV-2 and its B.1.1.7 mutant. MHC-I that best interacts with the proposed T cell epitopes were found, using immune epitope database. Molecular docking and molecular dynamic simulations were done for ensuring a good binding between the proposed MHC-I and T cell epitopes. The finally proposed T cell epitope was found to be antigenic, non-allergenic, non-toxic and stable. Further, the finally proposed B cell epitopes were also found to be antigenic. The population conservation analysis has ensured the presence of MHC-I molecule (respective to the finally proposed T cell) in human population of most affected countries with SARS-CoV-2. Thus the proposed T and B cell epitope could be effective in designing an epitope-based vaccine, which is effective on SARS-CoV-2 and its B.1.1.7mutant. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13721-021-00348-w.

Water activity and biomass estimation using digital image processing in solid-state fermentation.

Water activity in biotechnological applications plays a vital role. Estimation and precise control of water activity will enhance the product. The objective here is to use digital image processing technique in MATLAB for the quantification of the biomass and water condensate on a horizontal surface. A model has been developed with the data produced experimentally in this study in abiotic conditions. Also, a comparative study has been given for the estimation of the water condensate produced. It was observed that at a particular threshold value the error rate is less than 30%. The result of experimental study was good, and it showed a linear relation with proposed model. Also, the similar experimental estimation was done in biotic conditions, and results are showing good agreement between experimental observation and the model developed. Further, this method could be used in solid state fermentation process for water activity estimation and low-cost biomass estimation.

Insight into Structure-Function Relationships of ß-Lactamase and BLIPs Interface Plasticity using Protein-Protein Interactions.

BACKGROUND: Mostly BLIPs are identified in soil bacteria Streptomyces and originally isolated from Streptomyces clavuligerus and can be utilized as a model system for biophysical, structural, mutagenic and computational studies. BLIP possess homology with two proteins viz., BLIP-I (Streptomyces exofoliatus) and BLP (beta-lactamase inhibitory protein like protein from S. clavuligerus). BLIP consists of 165 amino acid, possessing two homologues domains comprising helix-loop-helix motif packed against four stranded beta-sheet resulting into solvent exposed concave surface with extended four stranded beta-sheet. BLIP-I is a 157 amino acid long protein obtained from S. exofoliatus having 37% sequence identity to BLIP and inhibits beta-lactamase. METHODS: This review is intended to briefly illustrate the beta-lactamase inhibitory activity of BLIP via proteinprotein interaction and aims to open up a new avenue to combat antimicrobial resistance using peptide based inhibition. RESULTS: D49A mutation in BLIP-I results in a decrease in affinity for TEM-1 from 0.5 nM to 10 nM (Ki). It is capable of inhibiting TEM-1 and bactopenemase and differs from BLIP only in modulating cell wall synthesis enzyme. Whereas, BLP is a 154 amino acid long protein isolated from S. clavuligerus via DNA sequencing analysis of Cephamycin-Clavulanate gene bunch. It shares 32% sequence similarity with BLIP and 42% with BLIP-I. Its biological function is unclear and lacks beta-lactamase inhibitory activity. CONCLUSION: Protein-protein interactions mediate a significant role in regulation and modulation of cellular developments and processes. Specific biological markers and geometric characteristics are manifested by active site binding clefts of protein surfaces which determines the specificity and affinity for their targets. TEM1.BLIP is a classical model to study protein-protein interaction. ß-Lactamase inhibitory proteins (BLIPs) interacts and inhibits various ß-lactamases with extensive range of affinities.