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Gurushankar K, Rimac H, Nadezhda P, Grishina M. Exploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method. J Biomol Struct Dyn 2023; 41:13963-13976. [PMID: 36762693 DOI: 10.1080/07391102.2023.2175727] [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: 10/07/2022] [Accepted: 01/29/2023] [Indexed: 02/11/2023]
Abstract
There is an urgent need to discover and develop novel drugs to combat Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) in humans. Alkaloids have been shown to have wide-ranging therapeutic application and could be ideal candidates for drug development, and research is underway to develop new anti-tubercular drugs from natural sources. In this regard, the current research deals with finding novel lead compounds from the Withania somnifera (WS) plant. Broad health benefits of WS are due to the presence of diverse chemical constituents which include anaferine and anahygrine and which belong to the alkaloid family. In the present study, these two compounds have been theoretically studied to understand their electronic properties using the density functional theory (DFT) at the B3LYP/6-311 + G (d,p) level. HOMO and LUMO properties and molecular electrostatic potential (MEP) surface were calculated. Further, to understand the mechanism of action of these compounds and to identify their putative drug target, molecular docking and dynamics studies were employed against Mycobacterium tuberculosis dihydrofolate reductase (DHFR). It was determined that NADP+ affects stability of the complexes by reducing fluctuations of residues 14-23 and 117-126. It was also found that Ile5 and Gln28 play an important role in complexation. Electron density analysis (using the AlteQ method) of the intermolecular region, analyzing both the anaferin-NADP+ and anahygrin-NADP+ complexes showed that anaferin and anahygrin complexes are more stable in the presence of NADP+. It has been established that in most intermolecular contacts the contribution of the ligand to the electron density is greater than that of NADP+. The present study thus provides an excellent way to analyze the effect of anaferine and anahygrine in essential processes of M. tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Krishnamoorthy Gurushankar
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, Tamilnadu, India
| | - Hrvoje Rimac
- Department of Medicinal Chemistry, University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Palko Nadezhda
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
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2
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Macnar JM, Brzezinski D, Chruszcz M, Gront D. Analysis of protein structures containing
HEPES
and
MES
molecules. Protein Sci 2022. [PMCID: PMC9601878 DOI: 10.1002/pro.4415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
X‐ray crystallography is the main experimental method behind ligand–macromolecule complexes found in the Protein Data Bank (PDB). Applying bioinformatics methods to such structural data can fuel drug discovery, albeit under the condition that the information is correct. Regrettably, a small number of structures in the PDB are of suboptimal quality due to incorrectly identified and modeled ligands in protein–ligand complexes. In this paper, we combine a theoretical‐graph approach, nuclear density estimates, bioinformatics methods, and prior chemical knowledge to analyze two non‐physiological ligands, HEPES and MES, that are frequent components of crystallization and purifications buffers. Our analysis includes quantum mechanics calculations and Cambridge Structure Database (CSD) queries to define the ideal conformation of these ligands, geometry analysis of PDB deposits regarding several quality factors, and a search for homologous structures to identify other small molecules that could bind in place of the parasitic ligand. Our results highlight the need for careful refinement of macromolecule–ligand complexes and better validation tools that integrate results from all relevant resources. PDB Code(s): 3K4L, 3PYI, 5T6L, 6BB0, 1PJX, 3O4P, 6WCF, 3DKE, 3E10, 6G38, 4E8R, 4Z91, 3E9F, 1MOS, 1MOQ, 2ESB, 1VHR, 4P66 and 6NNI;
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Affiliation(s)
- Joanna Magdalena Macnar
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- College of Inter‐Faculty Individual Studies in Mathematics and Natural Sciences University of Warsaw Warsaw Poland
- Faculty of Chemistry, Biological and Chemical Research Center University of Warsaw Warsaw Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- Institute of Computing Science Poznan University of Technology Poznan Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry University of South Carolina Columbia South Carolina USA
| | - Dominik Gront
- Department of Molecular Physiology and Biological Physics University of Virginia Charlottesville Virginia USA
- Faculty of Chemistry, Biological and Chemical Research Center University of Warsaw Warsaw Poland
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3
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Potency boost of a Mycobacterium tuberculosis dihydrofolate reductase inhibitor by multienzyme F 420H 2-dependent reduction. Proc Natl Acad Sci U S A 2021; 118:2025172118. [PMID: 34161270 PMCID: PMC8237569 DOI: 10.1073/pnas.2025172118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial metabolism can cause intrinsic drug resistance but can also convert inactive parent drugs into bioactive derivatives, as is the case for several antimycobacterial prodrugs. Here, we show that the intrabacterial metabolism of a Mtb dihydrofolate reductase (DHFR) inhibitor with moderate affinity for its target boosts its on-target activity by two orders of magnitude. This is a “prodrug-like” antimycobacterial that possesses baseline activity in the absence of intracellular bioactivation. By elucidating the metabolic enhancement mechanism, we have provided the basis for the rational optimization of a class of DHFR inhibitors and uncovered an antibacterial drug discovery concept. Triaza-coumarin (TA-C) is a Mycobacterium tuberculosis (Mtb) dihydrofolate reductase (DHFR) inhibitor with an IC50 (half maximal inhibitory concentration) of ∼1 µM against the enzyme. Despite this moderate target inhibition, TA-C shows exquisite antimycobacterial activity (MIC50, concentration inhibiting growth by 50% = 10 to 20 nM). Here, we investigated the mechanism underlying this potency disconnect. To confirm that TA-C targets DHFR and investigate its unusual potency pattern, we focused on resistance mechanisms. In Mtb, resistance to DHFR inhibitors is frequently associated with mutations in thymidylate synthase thyA, which sensitizes Mtb to DHFR inhibition, rather than in DHFR itself. We observed thyA mutations, consistent with TA-C interfering with the folate pathway. A second resistance mechanism involved biosynthesis of the redox coenzyme F420. Thus, we hypothesized that TA-C may be metabolized by Mtb F420–dependent oxidoreductases (FDORs). By chemically blocking the putative site of FDOR-mediated reduction in TA-C, we reproduced the F420-dependent resistance phenotype, suggesting that F420H2-dependent reduction is required for TA-C to exert its potent antibacterial activity. Indeed, chemically synthesized TA-C-Acid, the putative product of TA-C reduction, displayed a 100-fold lower IC50 against DHFR. Screening seven recombinant Mtb FDORs revealed that at least two of these enzymes reduce TA-C. This redundancy in activation explains why no mutations in the activating enzymes were identified in the resistance screen. Analysis of the reaction products confirmed that FDORs reduce TA-C at the predicted site, yielding TA-C-Acid. This work demonstrates that intrabacterial metabolism converts TA-C, a moderately active “prodrug,” into a 100-fold-more-potent DHFR inhibitor, thus explaining the disconnect between enzymatic and whole-cell activity.
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4
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Riboldi GP, Zigweid R, Myler PJ, Mayclin SJ, Couñago RM, Staker BL. Identification of P218 as a potent inhibitor of Mycobacterium ulcerans DHFR. RSC Med Chem 2021; 12:103-109. [PMID: 34046602 PMCID: PMC8130613 DOI: 10.1039/d0md00303d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/07/2020] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium ulcerans is the causative agent of Buruli ulcer, a debilitating chronic disease that mainly affects the skin. Current treatments for Buruli ulcer are efficacious, but rely on the use of antibiotics with severe side effects. The enzyme dihydrofolate reductase (DHFR) plays a critical role in the de novo biosynthesis of folate species and is a validated target for several antimicrobials. Here we describe the biochemical and structural characterization of M. ulcerans DHFR and identified P218, a safe antifolate compound in clinical evaluation for malaria, as a potent inhibitor of this enzyme. We expect our results to advance M. ulcerans DHFR as a target for future structure-based drug discovery campaigns.
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Affiliation(s)
- Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Rachael Zigweid
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
| | - Peter J Myler
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
- Department of Pediatrics, University of Washington Seattle Washington 91895 USA
| | - Stephen J Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID) Seattle Washington 98109 USA
- UCB Bainbridge Island Washington 98110 USA
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP) Campinas SP 13083-875 Brazil
- Structural Genomics Consortium, Departamento de Genética e Evolução, Instituto de Biologia, UNICAMP Campinas SP 13083-886 Brazil
| | - Bart L Staker
- Center for Infectious Disease Research, Seattle Children's Research Institute Seattle Washington 98109 USA
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5
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Eck T, Patel S, Candela T, Leon H K, Little M, Reis NE, Liyanagunawardana U, Gubler U, Janson CA, Catalano J, Goodey NM. Mutational analysis confirms the presence of distal inhibitor-selectivity determining residues in B. stearothermophilus dihydrofolate reductase. Arch Biochem Biophys 2020; 692:108545. [PMID: 32810476 PMCID: PMC10727455 DOI: 10.1016/j.abb.2020.108545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 11/20/2022]
Abstract
Many antibacterial and antiparasitic drugs work by competitively inhibiting dihydrofolate reductase (DHFR), a vital enzyme in folate metabolism. The interactions between inhibitors and DHFR active site residues are known in many homologs but the contributions from distal residues are less understood. Identifying distal residues that aid in inhibitor binding can improve targeted drug development programs by accounting for distant influences that may be less conserved and subject to frequent resistance causing mutations. Previously, a novel, homology-based, computational approach that mines ligand inhibition data was used to predict residues involved in inhibitor selectivity in the DHFR family. Expectedly, some inhibitor selectivity determining residue positions were predicted to lie in the active site and coincide with experimentally known inhibitor selectivity determining positions. However, other residues that group spatially in clusters distal to the active site have not been previously investigated. In this study, the effect of introducing amino acid substitutions at one of these predicted clusters (His38-Ala39-Ile40) on the inhibitor selectivity profile in Bacillus stearothermophilus dihydrofolate reductase (Bs DHFR) was investigated. Mutations were introduced into these cluster positions to change sidechain chemistry and size. We determined kcat and KM values and measured KD values at equilibrium for two competitive DHFR inhibitors, trimethoprim (TMP) and pyrimethamine (PYR). Mutations in the His38-Ala39-Ile40 cluster significantly impacted inhibitor binding and TMP/PYR selectivity - seven out of nine mutations resulted in tighter binding to PYR when compared to TMP. These data suggest that the His38-Ala39-Ile40 cluster is a distal inhibitor selectivity determining region that favors PYR binding in Bs DHFR and, possibly, throughout the DHFR family.
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Affiliation(s)
- Tyler Eck
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Seema Patel
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Thomas Candela
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Katherine Leon H
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Michael Little
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Natalia E Reis
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | | | - Ueli Gubler
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Cheryl A Janson
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Jaclyn Catalano
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Nina M Goodey
- Dept. of Chemistry & Biochemistry, Montclair State University, Montclair, NJ, 07043, USA.
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6
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Ribeiro JA, Hammer A, Libreros-Zúñiga GA, Chavez-Pacheco SM, Tyrakis P, de Oliveira GS, Kirkman T, El Bakali J, Rocco SA, Sforça ML, Parise-Filho R, Coyne AG, Blundell TL, Abell C, Dias MVB. Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase from Mycobacterium tuberculosis. ACS Infect Dis 2020; 6:2192-2201. [PMID: 32603583 DOI: 10.1021/acsinfecdis.0c00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Dihydrofolate reductase (DHFR), a key enzyme involved in folate metabolism, is a widely explored target in the treatment of cancer, immune diseases, bacteria, and protozoa infections. Although several antifolates have proved successful in the treatment of infectious diseases, they have been underexplored to combat tuberculosis, despite the essentiality of M. tuberculosis DHFR (MtDHFR). Herein, we describe an integrated fragment-based drug discovery approach to target MtDHFR that has identified hits with scaffolds not yet explored in any previous drug design campaign for this enzyme. The application of a SAR by catalog strategy of an in house library for one of the identified fragments has led to a series of molecules that bind to MtDHFR with low micromolar affinities. Crystal structures of MtDHFR in complex with compounds of this series demonstrated a novel binding mode that considerably differs from other DHFR antifolates, thus opening perspectives for the development of relevant MtDHFR inhibitors.
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Affiliation(s)
- João A. Ribeiro
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1474, São Paulo, SP 05508-000, Brazil
- Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, CEP, Campinas, SP 13083-862, Brazil
| | - Alexander Hammer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Gerardo A. Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1474, São Paulo, SP 05508-000, Brazil
- Department of Biology, IBILCE-State University of São Paulo, Rua Cristóvão Colombo, 2265, J. Nazareth, São José do Rio Preto, SP 15054-000, Brazil
- Department of Microbiology, University of Valle, Calle 4B # 36-00, Cali 760043, Colombia
| | - Sair M. Chavez-Pacheco
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1474, São Paulo, SP 05508-000, Brazil
| | - Petros Tyrakis
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Gabriel S. de Oliveira
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1474, São Paulo, SP 05508-000, Brazil
| | - Timothy Kirkman
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Jamal El Bakali
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Silvana A. Rocco
- National Laboratory of Biosciences, Rua Giuseppe Máximo Scolfaro, 10000, Campinas, SP 13083-100, Brazil
| | - Mauricio L. Sforça
- National Laboratory of Biosciences, Rua Giuseppe Máximo Scolfaro, 10000, Campinas, SP 13083-100, Brazil
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 580, São Paulo, SP 05508-000, Brazil
| | - Anthony G. Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Marcio V. B. Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes, 1474, São Paulo, SP 05508-000, Brazil
- Institute of Biology, University of Campinas, Cidade Universitária Zeferino Vaz, CEP, Campinas, SP 13083-862, Brazil
- Department of Biology, IBILCE-State University of São Paulo, Rua Cristóvão Colombo, 2265, J. Nazareth, São José do Rio Preto, SP 15054-000, Brazil
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
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7
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Kronenberger T, Ferreira GM, de Souza ADF, da Silva Santos S, Poso A, Ribeiro JA, Tavares MT, Pavan FR, Trossini GHG, Dias MVB, Parise-Filho R. Design, synthesis and biological activity of novel substituted 3-benzoic acid derivatives as MtDHFR inhibitors. Bioorg Med Chem 2020; 28:115600. [DOI: 10.1016/j.bmc.2020.115600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/02/2020] [Accepted: 06/16/2020] [Indexed: 10/24/2022]
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