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Rasul HO, Ghafour DD, Aziz BK, Hassan BA, Rashid TA, Kivrak A. Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners. Appl Biochem Biotechnol 2025; 197:1453-1503. [PMID: 39630336 DOI: 10.1007/s12010-024-05110-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2024] [Indexed: 03/29/2025]
Abstract
The drug development process is a critical challenge in the pharmaceutical industry due to its time-consuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable time. While valid, traditional methods such as in vivo and in vitro approaches are limited in their ability to analyze vast amounts of data efficiently, leading to wasteful outcomes. To expedite and streamline drug development, an increasing reliance on computer-aided drug design (CADD) approaches has merged. These sophisticated in silico methods offer a promising avenue for efficiently identifying viable drug candidates, thus providing pharmaceutical firms with significant opportunities to uncover new prospective drug targets. The main goal of this work is to review in silico methods used in the drug development process with a focus on identifying therapeutic targets linked to specific diseases at the genetic or protein level. This article thoroughly discusses A-to-Z in silico techniques, which are essential for identifying the targets of bioactive compounds and their potential therapeutic effects. This review intends to improve drug discovery processes by illuminating the state of these cutting-edge approaches, thereby maximizing the effectiveness and duration of clinical trials for novel drug target investigation.
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Affiliation(s)
- Hezha O Rasul
- Department of Pharmaceutical Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq.
| | - Dlzar D Ghafour
- Department of Medical Laboratory Science, College of Science, Komar University of Science and Technology, 46001, Sulaimani, Iraq
- Department of Chemistry, College of Science, University of Sulaimani, 46001, Sulaimani, Iraq
| | - Bakhtyar K Aziz
- Department of Nanoscience and Applied Chemistry, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq
| | - Bryar A Hassan
- Computer Science and Engineering Department, School of Science and Engineering, University of Kurdistan Hewler, KRI, Iraq
- Department of Computer Science, College of Science, Charmo University, Peshawa Street, Chamchamal, 46023, Sulaimani, Iraq
| | - Tarik A Rashid
- Computer Science and Engineering Department, School of Science and Engineering, University of Kurdistan Hewler, KRI, Iraq
| | - Arif Kivrak
- Department of Chemistry, Faculty of Sciences and Arts, Eskisehir Osmangazi University, Eskişehir, 26040, Turkey
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2
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Mourabiti F, Jouga F, Sakoui S, El Hosayny O, Zouheir Y, Soukri A, El Khalfi B. Mechanisms, therapeutic strategies, and emerging therapeutic alternatives for carbapenem resistance in Gram-negative bacteria. Arch Microbiol 2025; 207:58. [PMID: 39948320 DOI: 10.1007/s00203-025-04252-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 01/15/2025] [Accepted: 01/17/2025] [Indexed: 03/04/2025]
Abstract
Carbapenem-resistant Gram-negative bacteria (CR-GNB) have experienced an alarming surge in prevalence in recent years, escalating into a critical global healthcare crisis. As carbapenems represent the last line of defense against such pathogens, infections caused by CR-GNB have become increasingly challenging to treat, given the restricted therapeutic options and heightened mortality risks. The discovery and development of alternative therapeutic strategies that present novel avenues against multi-drug-resistant organisms are gaining increased attention, presenting a pressing need for innovative solutions. Our comprehensive review delves into the multifaceted landscape of carbapenem resistance in Gram-negative bacteria in response to this urgent challenge. The scope of this review aims to provide an up-to-date and in-depth exploration regarding the mode of action of carbapenem and the resisting mechanisms of carbapenem in GNB. Additionally, it discusses the state of the art of some clinical therapies for the treatment of infections caused by CR-GNB. Moreover, it describes several combinational and alternative therapies to combat CR-GNB, including the computational approach of "molecular docking". In light of the conclusions of this review, we call for the implementation of these strategies to develop comprehensive approaches to mitigate carbapenem resistance in Gram-negative bacteria.
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Affiliation(s)
- Fatima Mourabiti
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Research Center of Health & Biotechnology, Hassan II University of Casablanca, 20100, Casablanca, Morocco
| | - Fatimazahra Jouga
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Research Center of Health & Biotechnology, Hassan II University of Casablanca, 20100, Casablanca, Morocco
| | - Souraya Sakoui
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Research Center of Health & Biotechnology, Hassan II University of Casablanca, 20100, Casablanca, Morocco
| | - Otmane El Hosayny
- Applied Language and Culture Studies Laboratory, Faculty of Letters and Human Sciences, Chouaib Doukkali University, 24000, El Jadida, Morocco
| | - Yassine Zouheir
- Laboratory of Molecular Bacteriology, Pasteur Institute, Casablanca, Morocco
| | - Abdelaziz Soukri
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Research Center of Health & Biotechnology, Hassan II University of Casablanca, 20100, Casablanca, Morocco
| | - Bouchra El Khalfi
- Laboratory of Physiopathology, Molecular Genetics & Biotechnology, Faculty of Sciences Ain Chock, Research Center of Health & Biotechnology, Hassan II University of Casablanca, 20100, Casablanca, Morocco.
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Santana K, do Nascimento LD, Lima e Lima A, Damasceno V, Nahum C, Braga RC, Lameira J. Applications of Virtual Screening in Bioprospecting: Facts, Shifts, and Perspectives to Explore the Chemo-Structural Diversity of Natural Products. Front Chem 2021; 9:662688. [PMID: 33996755 PMCID: PMC8117418 DOI: 10.3389/fchem.2021.662688] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Natural products are continually explored in the development of new bioactive compounds with industrial applications, attracting the attention of scientific research efforts due to their pharmacophore-like structures, pharmacokinetic properties, and unique chemical space. The systematic search for natural sources to obtain valuable molecules to develop products with commercial value and industrial purposes remains the most challenging task in bioprospecting. Virtual screening strategies have innovated the discovery of novel bioactive molecules assessing in silico large compound libraries, favoring the analysis of their chemical space, pharmacodynamics, and their pharmacokinetic properties, thus leading to the reduction of financial efforts, infrastructure, and time involved in the process of discovering new chemical entities. Herein, we discuss the computational approaches and methods developed to explore the chemo-structural diversity of natural products, focusing on the main paradigms involved in the discovery and screening of bioactive compounds from natural sources, placing particular emphasis on artificial intelligence, cheminformatics methods, and big data analyses.
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Affiliation(s)
- Kauê Santana
- Instituto de Biodiversidade, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | | | - Anderson Lima e Lima
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Vinícius Damasceno
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | - Claudio Nahum
- Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
| | | | - Jerônimo Lameira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases. Sci Rep 2020; 10:12763. [PMID: 32728062 PMCID: PMC7391774 DOI: 10.1038/s41598-020-69431-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria are known to evade β-lactam antibiotic action by producing β-lactamases (BLs), including carbapenemases, which are able to hydrolyze nearly all available β-lactams. The production of BLs represents one of the best known and most targeted mechanisms of resistance in bacteria. We have performed the parallel screening of commercially available compounds against a panel of clinically relevant BLs: class A CTX-M-15 and KPC-2, subclass B1 NDM-1 and VIM-2 MBLs, and the class C P. aeruginosa AmpC. The results show that all BLs prefer scaffolds having electron pair donors: KPC-2 is preferentially inhibited by sulfonamide and tetrazole-based derivatives, NDM-1 by compounds bearing a thiol, a thiosemicarbazide or thiosemicarbazone moiety, while VIM-2 by triazole-containing molecules. Few broad-spectrum BLs inhibitors were identified; among these, compound 40 potentiates imipenem activity against an NDM-1-producing E. coli clinical strain. The binary complexes of the two most promising compounds binding NDM-1 and VIM-2 were obtained at high resolution, providing strong insights to improve molecular docking simulations, especially regarding the interaction of MBLs with inhibitors.
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Targeting the Class A Carbapenemase GES-5 via Virtual Screening. Biomolecules 2020; 10:biom10020304. [PMID: 32075131 PMCID: PMC7072645 DOI: 10.3390/biom10020304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/29/2022] Open
Abstract
The worldwide spread of β-lactamases able to hydrolyze last resort carbapenems contributes to the antibiotic resistance problem and menaces the successful antimicrobial treatment of clinically relevant pathogens. Class A carbapenemases include members of the KPC and GES families. While drugs against KPC-type carbapenemases have recently been approved, for GES-type enzymes, no inhibitors have yet been introduced in therapy. Thus, GES carbapenemases represent important drug targets. Here, we present an in silico screening against the most prevalent GES carbapenemase, GES-5, using a lead-like compound library of commercially available compounds. The most promising candidates were selected for in vitro validation in biochemical assays against recombinant GES-5 leading to four derivatives active as high micromolar competitive inhibitors. For the best inhibitors, the ability to inhibit KPC-2 was also evaluated. The discovered inhibitors constitute promising starting points for hit to lead optimization.
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Bellio P, Mancini A, Di Pietro L, Cracchiolo S, Franceschini N, Reale S, de Angelis F, Perilli M, Amicosante G, Spyrakis F, Tondi D, Cendron L, Celenza G. Inhibition of the transcriptional repressor LexA: Withstanding drug resistance by inhibiting the bacterial mechanisms of adaptation to antimicrobials. Life Sci 2019; 241:117116. [PMID: 31790690 DOI: 10.1016/j.lfs.2019.117116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/27/2019] [Indexed: 10/25/2022]
Abstract
AIMS LexA protein is a transcriptional repressor which regulates the expression of more than 60 genes belonging to the SOS global regulatory network activated by damages to bacterial DNA. Considering its role in bacteria, LexA represents a key target to counteract bacterial resistance: the possibility to modulate SOS response through the inhibition of LexA autoproteolysis may lead to reduced drug susceptibility and acquisition of resistance in bacteria. In our study we investigated boron-containing compounds as potential inhibitors of LexA self-cleavage. MAIN METHODS The inhibition of LexA self-cleavage was evaluated by following the variation of the first-order rate constant by LC-MS at several concentrations of inhibitors. In silico analysis was applied to predict the binding orientations assumed by the inhibitors in the protein active site, upon covalent binding to the catalytic Ser-119. Bacterial filamentation assay was used to confirm the ability of (3-aminophenyl)boronic acid to interfere with SOS induced activation. KEY FINDINGS Boron-containing compounds act as inhibitors of LexA self-cleavage, as also confirmed by molecular modelling where the compounds interact with the catalytic Ser-119, via the formation of an acyl-enzyme intermediate. A new equation for the description of the inhibition potency in an autoproteolytic enzyme is also disclosed. Bacterial filamentation assays strongly support the interference of our compounds with the SOS response activation through inhibition of septum formation. SIGNIFICANCE The obtained results demonstrated that phenylboronic compounds could be exploited in a hit-to-lead optimization process toward effective LexA self-cleavage inhibitors. They would sustain the rehabilitation in therapy of several dismissed antibiotics.
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Affiliation(s)
- Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Alisia Mancini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Letizia Di Pietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Salvatore Cracchiolo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Nicola Franceschini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Samantha Reale
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesco de Angelis
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Torino, Torino, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Padova, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy.
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Linciano P, Vicario M, Kekez I, Bellio P, Celenza G, Martín-Blecua I, Blázquez J, Cendron L, Tondi D. Phenylboronic Acids Probing Molecular Recognition against Class A and Class C β-lactamases. Antibiotics (Basel) 2019; 8:antibiotics8040171. [PMID: 31574990 PMCID: PMC6963673 DOI: 10.3390/antibiotics8040171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/24/2022] Open
Abstract
Worldwide dissemination of pathogens resistant to almost all available antibiotics represent a real problem preventing efficient treatment of infectious diseases. Among antimicrobial used in therapy, β-lactam antibiotics represent 40% thus playing a crucial role in the management of infections treatment. We report a small series of phenylboronic acids derivatives (BAs) active against class A carbapenemases KPC-2 and GES-5, and class C cephalosporinases AmpC. The inhibitory profile of our BAs against class A and C was investigated by means of molecular docking, enzyme kinetics and X-ray crystallography. We were interested in the mechanism of recognition among class A and class C to direct the design of broad serine β-Lactamases (SBLs) inhibitors. Molecular modeling calculations vs GES-5 and crystallographic studies vs AmpC reasoned, respectively, the ortho derivative 2 and the meta derivative 3 binding affinity. The ability of our BAs to protect β-lactams from BLs hydrolysis was determined in biological assays conducted against clinical strains: Fractional inhibitory concentration index (FICI) tests confirmed their ability to be synergic with β-lactams thus restoring susceptibility to meropenem. Considering the obtained results and the lack of cytotoxicity, our derivatives represent validated probe for the design of SBLs inhibitors.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Mattia Vicario
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100 L'Aquila, Italy.
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, via Vetoio 1, 67100 L'Aquila, Italy.
| | | | - Jesús Blázquez
- National Center of Biotechnology-CSIC, Calle Darwin 3, 28049 Madrid, Spain.
| | - Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy.
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
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Pemberton OA, Jaishankar P, Akhtar A, Adams JL, Shaw LN, Renslo AR, Chen Y. Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J Med Chem 2019; 62:8480-8496. [PMID: 31483651 DOI: 10.1021/acs.jmedchem.9b00728] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gram-negative pathogens expressing serine β-lactamases (SBLs) and metallo-β-lactamases (MBLs), especially those with carbapenemase activity, threaten the clinical utility of almost all β-lactam antibiotics. Here we describe the discovery of a heteroaryl phosphonate scaffold that exhibits noncovalent cross-class inhibition of representative carbapenemases, specifically the SBL KPC-2 and the MBLs NDM-1 and VIM-2. The most potent lead, compound 16, exhibited low nM to low μM inhibition of KPC-2, NDM-1, and VIM-2. Compound 16 potentiated imipenem efficacy against resistant clinical and laboratory bacterial strains expressing carbapenemases while showing some cytotoxicity toward human HEK293T cells only at concentrations above 100 μg/mL. Complex structures with KPC-2, NDM-1, and VIM-2 demonstrate how these inhibitors achieve high binding affinity to both enzyme classes. These findings provide a structurally and mechanistically new scaffold for drug discovery targeting multidrug resistant Gram-negative pathogens and more generally highlight the active site features of carbapenemases that can be leveraged for lead discovery.
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Affiliation(s)
- Orville A Pemberton
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Afroza Akhtar
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
| | - Jessie L Adams
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology & Molecular Biology , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center , University of California, San Francisco , 600 16th Street, Genentech Hall N574 , San Francisco , California 94158 , United States
| | - Yu Chen
- Department of Molecular Medicine , University of South Florida Morsani College of Medicine , 12901 Bruce B. Downs Boulevard, MDC 3522 , Tampa , Florida 33612 , United States
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Torelli NJ, Akhtar A, DeFrees K, Jaishankar P, Pemberton OA, Zhang X, Johnson C, Renslo AR, Chen Y. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. ACS Infect Dis 2019; 5:1013-1021. [PMID: 30942078 DOI: 10.1021/acsinfecdis.9b00052] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Serine and metallo-carbapenemases are a serious health concern due to their capability to hydrolyze nearly all β-lactam antibiotics. However, the molecular basis for their unique broad-spectrum substrate profile is poorly understood, particularly for serine carbapenemases, such as KPC-2. Using substrates and newly identified small molecules, we compared the ligand binding properties of KPC-2 with the noncarbapenemase CTX-M-14, both of which are Class A β-lactamases with highly similar active sites. Notably, compared to CTX-M-14, KPC-2 was more potently inhibited by hydrolyzed β-lactam products (product inhibition), as well as by a series of novel tetrazole-based inhibitors selected from molecular docking against CTX-M-14. Together with complex crystal structures, these data suggest that the KPC-2 active site has an enhanced ability to form favorable interactions with substrates and small molecule ligands due to its increased hydrophobicity and flexibility. Such properties are even more pronounced in metallo-carbapenemases, such as NDM-1, which was also inhibited by some of the novel tetrazole compounds, including one displaying comparable low μM affinities against both KPC-2 and NDM-1. Our results suggest that carbapenemase activity confers an evolutionary advantage on producers via a broad β-lactam substrate scope but also a mechanistic Achilles' heel that can be exploited for new inhibitor discovery. The complex structures demonstrate, for the first time, how noncovalent inhibitors can be engineered to simultaneously target both serine and metallo-carbapenemases. Despite the relatively modest activity of the current compounds, these studies also demonstrate that hydrolyzed products and tetrazole-based chemotypes can provide valuable starting points for broad-spectrum inhibitor discovery against carbapenemases.
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Affiliation(s)
- Nicholas J. Torelli
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Afroza Akhtar
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Kyle DeFrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Cody Johnson
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 600 16th Street, Genentech Hall N572B, San Francisco, California 94158, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
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Cendron L, Quotadamo A, Maso L, Bellio P, Montanari M, Celenza G, Venturelli A, Costi MP, Tondi D. X-ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid β-Lactamase Inhibitors. ACS Med Chem Lett 2019; 10:650-655. [PMID: 30996812 DOI: 10.1021/acsmedchemlett.8b00607] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/27/2019] [Indexed: 12/24/2022] Open
Abstract
Recent decades have witnessed a dramatic increase of multidrug resistant (MDR) bacteria, compromising the efficacy of available antibiotics, and a continual decline in the discovery of novel antibacterials. We recently reported the first library of benzo[b]thiophen-2-ylboronic acid inhibitors sharing broad spectrum activity against β-lactamases (BLs). The ability of these compounds to inhibit structurally and mechanistically different types of β-lactamases has been here structurally investigated. An extensive X-ray crystallographic analysis of boronic acids (BAs) binding to proteins representative of serine BLs (SBLs) and metallo β-lactamases (MBLs) have been conducted to depict the role played by the boronic group in driving molecular recognition, especially in the interaction with MBLs. Our derivatives are the first case of noncyclic boronic acids active against MBLs and represent a productive route toward potent broad-spectrum inhibitors.
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Affiliation(s)
- Laura Cendron
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Antonio Quotadamo
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Lorenzo Maso
- Department of Biology, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Pierangelo Bellio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy
| | - Martina Montanari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Giuseppe Celenza
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, via Vetoio 1, 67100 L’Aquila, Italy
| | | | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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