molecules Review Resistance of Gram-Negative Bacteria to Current Antibacterial Agents and Approaches to Resolve It Zeinab Breijyeh , Buthaina Jubeh and Rafik Karaman * Department of Bioorganic & Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Quds University, Jerusalem P.O. Box 20002, Palestine; [email protected] (Z.B.); [email protected] (B.J.) * Correspondence: [email protected] Received: 13 February 2020; Accepted: 12 March 2020; Published: 16 March 2020 Abstract: Antimicrobial resistance represents an enormous global health crisis and one of the most serious threats humans face today. Some bacterial strains have acquired resistance to nearly all antibiotics. Therefore, new antibacterial agents are crucially needed to overcome resistant bacteria. In 2017, the World Health Organization (WHO) has published a list of antibiotic-resistant priority pathogens, pathogens which present a great threat to humans and to which new antibiotics are urgently needed the list is categorized according to the urgency of need for new antibiotics as critical, high, and medium priority, in order to guide and promote research and development of new antibiotics. The majority of the WHO list is Gram-negative bacterial pathogens. Due to their distinctive structure, Gram-negative bacteria are more resistant than Gram-positive bacteria, and cause significant morbidity and mortality worldwide. Several strategies have been reported to fight and control resistant Gram-negative bacteria, like the development of antimicrobial auxiliary agents, structural modification of existing antibiotics, and research into and the study of chemical structures with new mechanisms of action and novel targets that resistant bacteria are sensitive to. Research efforts have been made to meet the urgent need for new treatments; some have succeeded to yield activity against resistant Gram-negative bacteria by deactivating the mechanism of resistance, like the action of the β-lactamase Inhibitor antibiotic adjuvants. Another promising trend was by referring to nature to develop naturally derived agents with antibacterial activity on novel targets, agents such as bacteriophages, DCAP(2-((3-(3,6-dichloro-9H-carbazol-9-yl)-2-hydroxypropyl)amino)-2(hydroxymethyl)propane1,3- diol, Odilorhabdins (ODLs), peptidic benzimidazoles, quorum sensing (QS) inhibitors, and metal-based antibacterial agents. Keywords: antimicrobial; antibiotic; resistance; Gram-negative; multidrug resistance (MDR); pathogens; bacteria; alternative therapies 1. Introduction Throughout history, natural products have been utilized to treat a variety of diseases; cinchona tree containing quinine to treat malaria, penicillin for the treatment of infectious diseases, and others. Since the discovery of penicillin by Fleming in 1929, a large number of antibacterial agents have been developed and have had a huge impact on human health and the mortality rates of humans around the world [1]. Widespread excessive dispensing and irresponsible use of antibiotics has resulted in the development of resistant strains. Unfortunately, most antibiotics are available over the counter in the developing countries and can be dispensed without prescription; therefore, patients and general public education are crucially needed [2]. Molecules 2020, 25, 1340; doi:10.3390/molecules25061340 www.mdpi.com/journal/molecules Molecules 2020, 25, 1340 2 of 23 MoleculesThe global 2020 e, ff25ort, x FOR to develop PEER REVIEW new antibiotics or modify existing ones to fight resistant pathogens2 of 25 globally is now huge. Antibiotic resistance evolves when the bacteria can escape the effect of antibioticscell, or modifying by diff erenttheir outer mechanisms, structure like resulting neutralizing in inhibition the antibiotics, of the drugs’ pumping attachment them to outside the bacteria. of the cell,The mechanisms or modifying of their antibiotic outer structureresistance resulting are categorized in inhibition into four of the groups: drugs’ intrinsic attachment resistance to the in bacteria. which Thebacteria mechanisms can change of antibiotic their structures resistance or are compon categorizedents, intoanother four groups:way is acquired intrinsic resistanceresistance, in where which bacteria cancan changeacquire their new structures resistance or components,genes and DN anotherA from way other is acquired resistant resistance, bacteria. whereFurthermore, bacteria cangenetic acquire changes new resistance in the DNA genes which and DNA can from alter other the resistantproduction bacteria. of protein Furthermore, leading genetic to different changes incomponents the DNA whichand receptors can alter that the productioncannot be ofrecognized protein leading by the to antibiotic, different componentsand finally DNA and receptors transfer thatthrough cannot a behorizontal recognized gene by thetransfer antibiotic, between and finally bacteria DNA via transfer transformation through a horizontalor transduction gene transfer or by betweenconjugation bacteria [3]. via transformation or transduction or by conjugation [3]. Resistance toto antimicrobialsantimicrobials isis aa growinggrowing crisis crisis in in clinical clinical medicine. medicine. In In 2017, 2017, the the WHO WHO published published a lista list of bacteriaof bacteria where where new new antibiotics antibiotics to tackle to tack themle arethem needed are urgentlyneeded urgently and grouped and themgrouped according them toaccording their priority to their as priority critical, high,as critical, and mediumhigh, and (Figure medium1). (Figure 1). Figure 1. WHO list of priority pathogens grouped under three priority categories according to Figure 1. WHO list of priority pathogens grouped under three priority categories according to their their antibiotic resistance: Critical, high and medium to encourage research and development of antibiotic resistance: Critical, high and medium to encourage research and development of new new antibiotics. antibiotics. Gram Negative Bacteria 1.1. Gram Negative Bacteria In 1884 Hans Christian Gram developed a method to distinguish between Gram-positive and Gram-negativeIn 1884 Hans bacteria Christian by using Gram a crystaldeveloped violet-iodine a method complex to distinguish and a safranin between counter Gram-positive stain. Gram- and positiveGram-negative bacteria bacteria stained by violet using or a purple crystal and violet-iodine Gram-negative complex bacteria and a don’tsafranin retain counter the complex stain. Gram- stain andpositive counter bacteria stain stained with safranin violet or to purple give a pinkand Gram-negative color. This diff erencebacteria is don’t due to retain the composition the complex or stain the morphologyand counter stain of the with cell wallsafranin in each to give bacterial a pink type color. [1, 2This]. difference is due to the composition or the morphology of the cell wall in each bacterial type [1,2]. Gram-negative bacteria have an envelope that consists of three layers (Figure 2).The first layer is the outer membrane (OM), a protective and a unique feature that distinguishes Gram-negative bacteria from Gram-positive bacteria. The OM has phospholipids that are bound to the inner leaflet Molecules 2020, 25, 1340 3 of 23 MoleculesGram-negative 2020, 25, x bacteria FOR PEER have REVIEW an envelope that consists of three layers (Figure2).The first layer3 of is25 the outer membrane (OM), a protective and a unique feature that distinguishes Gram-negative bacteria fromof the Gram-positive membrane, and bacteria. lipopolysaccharide The OM has (LPS) phospholipids bound to the that outer are boundleaflet towhich the inneris known leaflet to ofcause the membrane,endotoxic shock. and lipopolysaccharide Moreover, the OM (LPS) contains bound protei to thens outer called leaflet the outer which memb is knownrane to proteins cause endotoxic (OMPs) shock.such as Moreover,porins and the others OM which contains allow proteins the passage called theof small outer molecules membrane like proteins amino (OMPs)acids and such small as porinssaccharides. and others The whichsecond allow layer the is passagethe peptidoglyca of small moleculesn cell wall like which amino is acids a rigid and smallexoskeleton saccharides. that Thedetermines second the layer cell is shape the peptidoglycan and consists cellof a wallrepeat which unit isof a the rigid disaccharide exoskeleton N-acetyl that determines glucosamine-N- the cell shapeacetylmuramic and consists acid of [3]. a repeat The third unit oflayer the is disaccharide the inner membrane N-acetyl glucosamine-N-acetylmuramic (IM) which is a phospholipid acidbilayer [3]. Thethat thirdis responsible layer is thefor innermultifunctional membrane processes (IM) which likeis structure, a phospholipid transport, bilayer and biosynthetic that is responsible functions. for multifunctionalIn addition, it is processes the site likefor structure,DNA anchoring transport, and and plays biosynthetic an important functions. role Inin addition,sister chromosomes it is the site forseparation DNA anchoring [4]. and plays an important role in sister chromosomes separation [4]. Figure 2. A diagram describes the cell wall st structureructure of Gram-negative bacteria. The outer membrane of Gram-negative bacteria is the main reason for resistance to a wide range of antibiotics including ββ-lactams, quinilons, colistins and otherother antibiotics.antibiotics. Most antibiotics must pass thethe outerouter membranemembrane toto access access their their targets, targets, for for example, example, hydrophobic hydrophobic