Inhibition of β-lactamase function by de novo designed peptide

PLOS ONE RESEARCH ARTICLE Inhibition of β-lactamase function by de novo designed peptide Arunima Mishra ID1*, Irena Cosic2, Ivan Loncarevic3, Drasko Cosic2, Hansel M. Fletcher1* 1 Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, United States America, 2 AMALNA Consulting, Black Rock, Melbourne, VIC, Australia, 3 QuantBioRes-QBR A/S, Copenhagen, Denmark * (AM); (HMF) a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Mishra A, Cosic I, Loncarevic I, Cosic D, Fletcher HM (2023) Inhibition of β-lactamase function by de novo designed peptide. PLoS ONE 18(9): e0290845. https://doi.org/10.1371/journal. pone.0290845 Editor: Farah Al-Marzooq, UAE University: United Arab Emirates University, UNITED ARAB EMIRATES Received: May 12, 2023 Accepted: August 16, 2023 Published: September 8, 2023 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0290845 Copyright: © 2023 Mishra et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All data generated or analyzed during this study are included in the published article. The detailed sequences of peptides pep1-4 are not included in the article due Abstract Antimicrobial resistance is a great public health concern that is now described as a “silent pandemic”. The global burden of antimicrobial resistance requires new antibacterial treatments, especially for the most challenging multidrug-resistant bacteria. There are various mechanisms by which bacteria develop antimicrobial resistance including expression of βlactamase enzymes, overexpression of efflux pumps, reduced cell permeability through downregulation of porins required for β-lactam entry, or modifications in penicillin-binding proteins. Inactivation of the β-lactam antibiotics by β-lactamase enzymes is the most common mechanism of bacterial resistance to these agents. Although several effective smallmolecule inhibitors of β-lactamases such as clavulanic acid and avibactam are clinically available, they act only on selected class A, C, and some class D enzymes. Currently, none of the clinically approved inhibitors can effectively inhibit Class B metallo-β-lactamases. Additionally, there is increased resistance to these inhibitors reported in several bacteria. The objective of this study is to use the Resonant Recognition Model (RRM), as a novel strategy to inhibit/modulate specific antimicrobial resistance targets. The RRM is a bio-physical approach that analyzes the distribution of energies of free electrons and posits that there is a significant correlation between the spectra of this energy distribution and related protein biological activity. In this study, we have used the RRM concept to evaluate the structure-function properties of a group of 22 β-lactamase proteins and designed 30-mer peptides with the desired RRM spectral periodicities (frequencies) to function as β-lactamase inhibitors. In contrast to the controls, our results indicate 100% inhibition of the class A β-lactamases from Escherichia coli and Enterobacter cloacae. Taken together, the RRM model can likely be utilized as a promising approach to design β-lactamase inhibitors for any specific class. This may open a new direction to combat antimicrobial resistance. Introduction The discovery of penicillin by Alexander Fleming in 1929 is one of the major biomedical breakthroughs in human history [1]. Since then, antibiotics have been recognized as a powerful drug and have directly saved numerous lives by enabling the treatment of once-common PLOS ONE | https://doi.org/10.1371/journal.pone.0290845 September 8, 2023 1 / 15 PLOS ONE to unresolved intellectual property challenges. The authors are willing to share the sequences in response to individual requests to Hansel Fletcher [] and/or Ivan Loncarevic []. Funding: RRM analysis, peptide design and peptide synthesis were financed by QuantBioResQBR A/S. Work on testing of peptides was supported by Public Health Services Grants DE030411 and DE025852 from NIDCR (to HMF) and DE029825 (to AM). The funder NIDCR had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. β-lactamase activity inhibiting peptide causes of death such as pneumonia and sepsis. In addition, its use has had a significant positive impact on a range of healthcare interventions such as surgery, chemotherapy, and organ transplants [2,3]. β-lactam antibiotics are the most often used antimicrobial agents and continue to play a central role in treating bacterial infections [4,5]. These drugs have a highly reactive βlactam ring in their structure. At present, penicillins, cephalosporins, carbapenems and monobactams are the four main classes of β-lactam antibiotics in clinical use. They cause cell death by interrupting bacterial cell-wall formation by binding to essential penicillin-binding proteins, enzymes that are involved in the terminal steps of peptidoglycan cross-linking, in both Gram-positive and Gram-negative bacteria [6,7]. Like other antimicrobial classes, the widespread and excess use of β-lactams in clinical practice have led to antibiotic resistance in bacteria with a resultant big burden and extra cost on health-delivery systems [8]. In the last 15 years, the problem of antibiotic resistance to two or more drugs (multidrug-resistance) has increased exponentially, thus, challenging the management of severe healthcare-associated infections, increasing morbidity and mortality, and generating strains with extreme resistance [9,10]. More than 2.8 million antimicrobial-resistant infections, linked to nearly 35,000 deaths at a healthcare cost of approximately 2 billion dollars, have been recently reported in the United States of America [11]. The World Health Organization (WHO) has predicted that by 2050 deaths associated with multidrug-resistant bacteria will be 10 million people a year which is greater than the current global deaths due to all cancers (8.2 million) costing up to $100 trillion [12]. The antimicrobial resistance mechanisms involve both enzymatic and non-enzymatic reactions. The enzymatic mechanism includes the expression of enzymes which can inactivate the antibiotic. Non-enzymatic mechanisms may result from non-transmissible mechanisms (disabling the drugs, overexpression of efflux pumps, reduced cell permeability through downregulation of porins required for β-la (...truncated)