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Lima AH, Silva JR, Alves C, Lameira J. QM/MM Study of the Fosfomycin Resistance Mechanism Involving FosB Enzyme. ACS OMEGA 2021; 6:12507-12512. [PMID: 34056400 PMCID: PMC8154160 DOI: 10.1021/acsomega.1c00096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/12/2021] [Indexed: 06/01/2023]
Abstract
Multidrug-resistant organisms contain antibiotic-modifying enzymes that facilitate resistance to a variety of antimicrobial compounds. Particularly, the fosfomycin (FOF) drug can be structurally modified by several FOF-modifying enzymes before it reaches the biological target. Among them, FosB is an enzyme that utilizes l-cysteine or bacillithiol in the presence of a divalent metal to open the epoxide ring of FOF and, consequently, inactivate the drug. Here, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of the reaction involving FosB and FOF. The calculated free-energy profiles show that the cost to open the epoxide ring of FOF at the C2 atom is ∼3.0 kcal/mol higher than that at the C1 atom. Besides, our QM/MM MD results revealed the critical role of conformation change of Cys9 and Asn50 to release the drug from the active site. Overall, the present study provides insights into the mechanism of FOF-resistant proteins.
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Affiliation(s)
- Anderson H. Lima
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - José Rogério
A. Silva
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - Cláudio
Nahum Alves
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento
e Desenvolvimento de Fármacos, Instituto de Ciências
Exatas e Naturais, Universidade Federal
do Pará, Rua Augusto Corrêa, 01, 66075-110, Belém, Pará, Brasil
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2
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Ntombela T, Seupersad A, Maseko S, Ibeji CU, Tolufashe G, Maphumulo SI, Naicker T, Baijnath S, Maguire GEM, Govender T, Lamichhane G, Honarparvar B, Kruger HG. Mechanistic insight on the inhibition of D, D-carboxypeptidase from Mycobacterium tuberculosis by β-lactam antibiotics: an ONIOM acylation study. J Biomol Struct Dyn 2021; 40:7645-7655. [PMID: 33719919 DOI: 10.1080/07391102.2021.1899052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Mycobacterium tuberculosis cell wall is intricate and impermeable to many agents. A D, D-carboxypeptidase (DacB1) is one of the enzymes involved in the biosynthesis of cell wall peptidoglycan and catalyzes the terminal D-alanine cleavage from pentapeptide precursors. Catalytic activity and mechanism by which DacB1 functions is poorly understood. Herein, we investigated the acylation mechanism of DacB1 by β-lactams using a 6-membered ring transition state model that involves a catalytic water molecule in the reaction pathway. The full transition states (TS) optimization plus frequency were achieved using the ONIOM (B3LYP/6-31 + G(d): AMBER) method. Subsequently, the activation free energies were computed via single-point calculations on fully optimized structures using B3LYP/6-311++(d,p): AMBER and M06-2X/6-311++(d,p): AMBER with an electronic embedding scheme. The 6-membered ring transition state is an effective model to examine the inactivation of DacB1 via acylation by β-lactams antibiotics (imipenem, meropenem, and faropenem) in the presence of the catalytic water. The ΔG# values obtained suggest that the nucleophilic attack on the carbonyl carbon is the rate-limiting step with 13.62, 19.60 and 30.29 kcal mol-1 for Imi-DacB1, Mero-DacB1 and Faro-DacB1, respectively. The electrostatic potential (ESP) and natural bond orbital (NBO) analysis provided significant electronic details of the electron-rich region and charge delocalization, respectively, based on the concerted 6-membered ring transition state. The stabilization energies of charge transfer within the catalytic reaction pathway concurred with the obtained activation free energies. The outcomes of this study provide important molecular insight into the inactivation of D, D-carboxypeptidase by β-lactams.
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Affiliation(s)
- Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anya Seupersad
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gideon Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Siyabonga Innocent Maphumulo
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, Richards Bay, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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3
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Apostolos AJ, Nelson JM, Silva JRA, Lameira J, Achimovich AM, Gahlmann A, Alves CN, Pires MM. Facile Synthesis and Metabolic Incorporation of m-DAP Bioisosteres Into Cell Walls of Live Bacteria. ACS Chem Biol 2020; 15:2966-2975. [PMID: 33078931 DOI: 10.1021/acschembio.0c00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bacterial cell walls contain peptidoglycan (PG), a scaffold that provides proper rigidity to resist lysis from internal osmotic pressure and a barrier to protect cells against external stressors. It consists of repeating sugar units with a linkage to a stem peptide that becomes cross-linked by cell wall transpeptidases (TP). While synthetic PG fragments containing l-lysine in the third position on the stem peptide are easier to access, those with meso-diaminopimelic acid (m-DAP) pose a severe synthetic challenge. Herein, we describe a solid phase synthetic scheme based on widely available building blocks to assemble meso-cystine (m-CYT), which mimics key structural features of m-DAP. To demonstrate proper mimicry of m-DAP, cell wall probes were synthesized with m-CYT in place of m-DAP and evaluated for their metabolic processing in live bacterial cells. We found that m-CYT-based cell wall probes were properly processed by TPs in various bacterial species that endogenously contain m-DAP in their PG. Additionally, we have used hybrid quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics (MD) simulations to explore the influence of m-DAP analogs on the PG cross-linking. The results showed that the cross-linking mechanism of transpeptidases occurred through a concerted process. We anticipate that this strategy, which is based on the use of inexpensive and commercially available building blocks, can be widely adopted to provide greater accessibility of PG mimics for m-DAP containing organisms.
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Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Julia M. Nelson
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Alecia M. Achimovich
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Andreas Gahlmann
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Cláudio N. Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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4
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Sanusi ZK, Lawal MM, Gupta PL, Govender T, Baijnath S, Naicker T, Maguire GEM, Honarparvar B, Roitberg AE, Kruger HG. Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation. J Biomol Struct Dyn 2020; 40:1736-1747. [PMID: 33073714 DOI: 10.1080/07391102.2020.1832578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
HIV-1 protease (HIV-1 PR) is an essential enzyme for the replication process of its virus, and therefore considered an important target for the development of drugs against the acquired immunodeficiency syndrome (AIDS). Our previous study shows that the catalytic mechanism of subtype B/C-SA HIV-1 PR follows a one-step concerted acyclic hydrolysis reaction process using a two-layered ONIOM B3LYP/6-31++G(d,p) method. This present work is aimed at exploring the proposed mechanism of the proteolysis catalyzed by HIV-1 PR and to ensure our proposed mechanism is not an artefact of a single theoretical technique. Hence, we present umbrella sampling method that is suitable for calculating potential mean force (PMF) for non-covalent ligand/substrate-enzyme association/dissociation interactions which provide thermodynamic details for molecular recognition. The free activation energy results were computed in terms of PMF analysis within the hybrid QM(DFTB)/MM approach. The theoretical findings suggest that the proposed mechanism corresponds in principle with experimental data. Given our observations, we suggest that the QM/MM MD method can be used as a reliable computational technique to rationalize lead compounds against specific targets such as the HIV-1 protease.
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Affiliation(s)
- Zainab K Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Monsurat M Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Pancham Lal Gupta
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | | | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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5
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Tolufashe GF, Sabe VT, Ibeji CU, Ntombela T, Govender T, Maguire GEM, Kruger HG, Lamichhane G, Honarparvar B. Structure and Function of L,D- and D,D-Transpeptidase Family Enzymes from Mycobacterium tuberculosis. Curr Med Chem 2020; 27:3250-3267. [PMID: 30501595 DOI: 10.2174/0929867326666181203150231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/28/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023]
Abstract
Peptidoglycan, the exoskeleton of bacterial cell and an essential barrier that protects the cell, is synthesized by a pathway where the final steps are catalysed by transpeptidases. Knowledge of the structure and function of these vital enzymes that generate this macromolecule in M. tuberculosis could facilitate the development of potent lead compounds against tuberculosis. This review summarizes the experimental and computational studies to date on these aspects of transpeptidases in M. tuberculosis that have been identified and validated. The reported structures of L,D- and D,D-transpeptidases, as well as their functionalities, are reviewed and the proposed enzymatic mechanisms for L,D-transpeptidases are summarized. In addition, we provide bioactivities of known tuberculosis drugs against these enzymes based on both experimental and computational approaches. Advancing knowledge about these prominent targets supports the development of new drugs with novel inhibition mechanisms overcoming the current need for new drugs against tuberculosis.
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Affiliation(s)
- Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Colins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Gyanu Lamichhane
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, United States
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
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6
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Silva JRA, Cianni L, Araujo D, Batista PHJ, de Vita D, Rosini F, Leitão A, Lameira J, Montanari CA. Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism. J Chem Inf Model 2020; 60:1666-1677. [PMID: 32126170 DOI: 10.1021/acs.jcim.9b01138] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reversible and irreversible covalent ligands are advanced cysteine protease inhibitors in the drug development pipeline. K777 is an irreversible inhibitor of cruzain, a necessary enzyme for the survival of the Trypanosoma cruzi (T. cruzi) parasite, the causative agent of Chagas disease. Despite their importance, irreversible covalent inhibitors are still often avoided due to the risk of adverse effects. Herein, we replaced the K777 vinyl sulfone group with a nitrile moiety to obtain a reversible covalent inhibitor (Neq0682) of cysteine protease. Then, we used advanced experimental and computational techniques to explore details of the inhibition mechanism of cruzain by reversible and irreversible inhibitors. The isothermal titration calorimetry (ITC) analysis shows that inhibition of cruzain by an irreversible inhibitor is thermodynamically more favorable than by a reversible one. The hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) simulations were used to explore the mechanism of the reaction inhibition of cruzain by K777 and Neq0682. The calculated free energy profiles show that the Cys25 nucleophilic attack and His162 proton transfer occur in a single step for a reversible inhibitor and two steps for an irreversible covalent inhibitor. The hybrid QM/MM calculated free energies for the inhibition reaction correspond to -26.7 and -5.9 kcal mol-1 for K777 and Neq0682 at the MP2/MM level, respectively. These results indicate that the ΔG of the reaction is very negative for the process involving K777, consequently, the covalent adduct cannot revert to a noncovalent protein-ligand complex, and its binding tends to be irreversible. Overall, the present study provides insights into a covalent inhibition mechanism of cysteine proteases.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos. Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, CEP 66075-110, Belém, Pará, Brazil
| | - Lorenzo Cianni
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Deborah Araujo
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Pedro Henrique Jatai Batista
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Daniela de Vita
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Fabiana Rosini
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Andrei Leitão
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos. Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Rua Augusto Corrêa 01, CEP 66075-110, Belém, Pará, Brazil
| | - Carlos A Montanari
- Medicinal Chemistry Group, Institute of Chemistry of São Carlos, University of São Paulo, Avenue Trabalhador Sancarlense 400, 23566-590, São Carlos, São Paulo, Brazil
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7
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Pereira PRM, Araújo JDO, Silva JRA, Alves CN, Lameira J, Lima AH. Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. J Chem Inf Model 2020; 60:738-746. [DOI: 10.1021/acs.jcim.9b01079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paulo R. M. Pereira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Jéssica de O. Araújo
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Cláudio N. Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
- Instituto de Ciências Biológicas, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110, Belém, PA, Brasil
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8
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Zhao F, Hou YJ, Zhang Y, Wang DC, Li DF. The 1-β-methyl group confers a lower affinity of l,d-transpeptidase Ldt Mt2 for ertapenem than for imipenem. Biochem Biophys Res Commun 2019; 510:254-260. [PMID: 30686533 DOI: 10.1016/j.bbrc.2019.01.082] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 11/19/2022]
Abstract
L,D-transpeptidases, widely distributed in bacteria and even in the difficult-to-treat ESKAPE pathogens, can confer antibacterial resistance against the traditional β-lactam antibiotics through bypass of the 4 → 3 transpeptide linkage. LdtMt2, a l,d-transpeptidase in Mycobacteria tuberculosis, is essential for bacterial virulence and is considered as a potential anti-tuberculosis target inhibited by carbapenems. Diverse interaction modes between carbapenems and LdtMt2 have been reported, there are only limited evidences to validate those interaction modes. Herein, we identified the stable binding states of two carbapenems, imipenem and ertapenem, via crystallographic and biochemical studies, discovered that they adopt similar binding conformations. We further demonstrate the absence of the 1-β-methyl group in imipenem and the presence of both Y308 and Y318 residues in LdtMt2 synergistically resulted in one order of magnitude higher affinity for imipenem than ertapenem. Our study provides a structural basis for the rational drug design and evolvement of novel carbapenems against bacterial L,D-transpeptidases.
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Affiliation(s)
- Fen Zhao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - De-Feng Li
- University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
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9
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Tolufashe GF, Halder AK, Ibeji CU, Lawal MM, Ntombela T, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. Inhibition of Mycobacterium tuberculosis
L,D-Transpeptidase 5 by Carbapenems: MD and QM/MM Mechanistic Studies. ChemistrySelect 2018. [DOI: 10.1002/slct.201803184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gideon F. Tolufashe
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Amit K. Halder
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Collins U. Ibeji
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Monsurat M. Lawal
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
- School of Chemistry and Physics; University of KwaZulu-Natal; 4001 Durban South Africa
| | - Gyanu Lamichhane
- Division of Infectious Diseases; School of Medicine; Johns Hopkins University; Baltimore MD 21205 USA
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit; School of Health Sciences; University of KwaZulu-Natal; Durban 4001 South Africa
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10
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Inhibition mechanism of L,D-transpeptidase 5 in presence of the β-lactams using ONIOM method. J Mol Graph Model 2018; 87:204-210. [PMID: 30554066 DOI: 10.1016/j.jmgm.2018.11.009] [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: 09/28/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB) is one of the world's deadliest diseases resulting from infection by the bacterium, Mycobacterium tuberculosis (M.tb). The L,D-transpeptidase enzymes catalyze the synthesis of 3 → 3 transpeptide linkages which are predominant in the peptidoglycan of the M.tb cell wall. Carbapenems is class of β-lactams that inactivate L,D-transpeptidases by acylation, although differences in antibiotic side chains modulate drug binding and acylation rates. Herein, we used a two-layered our Own N-layer integrated Molecular Mechanics ONIOM method to investigate the catalytic mechanism of L,D-transpeptidase 5 (LdtMt5) by β-lactam derivatives. LdtMt5 complexes with six β-lactams, ZINC03788344 (1), ZINC02462884 (2), ZINC03791246 (3), ZINC03808351 (4), ZINC03784242 (5) and ZINC02475683 (6) were simulated. The QM region (high-level) comprises the β-lactam, one water molecule and the Cys360 catalytic residue, while the rest of the LdtMt5 residues were treated with AMBER force field. The activation energies (ΔG#) were calculated with B3LYP, M06-2X and ωB97X density functionals with 6-311++G(2d, 2p) basis set. The ΔG# for the acylation of LdtMt5 by the selected β-lactams were obtained as 13.67, 20.90, 22.88, 24.29, 27.86 and 28.26 kcal mol-1respectively. Several of the compounds showed an improved ΔG# when compared to the previously calculated energies for imipenem and meropenem for the acylation step for LdtMt5. This model provides further validation of the catalytic inhibition mechanism of LDTs with atomistic detail.
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11
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Caballero J, Morales-Bayuelo A, Navarro-Retamal C. Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. J Comput Aided Mol Des 2018; 32:1315-1336. [PMID: 30367309 DOI: 10.1007/s10822-018-0173-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/20/2018] [Indexed: 12/17/2022]
Abstract
In the last decades, human protein kinases (PKs) have been relevant as targets in the development of novel therapies against many diseases, but the study of Mycobacterium tuberculosis PKs (MTPKs) involved in tuberculosis pathogenesis began much later and has not yet reached an advanced stage of development. To increase knowledge of these enzymes, in this work we studied the structural features of MTPKs, with focus on their ATP-binding sites and their interactions with inhibitors. PknA, PknB, and PknG are the most studied MTPKs, which were previously crystallized; ATP-competitive inhibitors have been designed against them in the last decade. In the current work, reported PknA, PknB, and PknG inhibitors were extracted from literature and their orientations inside the ATP-binding site were proposed by using docking method. With this information, interaction fingerprints were elaborated, which reveal the more relevant residues for establishing chemical interactions with inhibitors. The non-crystallized MTPKs PknD, PknF, PknH, PknJ, PknK, and PknL were also studied; their three-dimensional structural models were developed by using homology modeling. The main characteristics of MTPK ATP-binding sites (the non-crystallized and crystallized MTPKs, including PknE and PknI) were accounted; schemes of the main polar and nonpolar groups inside their ATP-binding sites were constructed, which are suitable for a major understanding of these proteins as antituberculotic targets. These schemes could be used for establishing comparisons between MTPKs and human PKs in order to increase selectivity of MTPK inhibitors. As a key tool for guiding medicinal chemists interested in the design of novel MTPK inhibitors, our work provides a map of the structural elements relevant for the design of more selective ATP-competitive MTPK inhibitors.
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Affiliation(s)
- Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile.
| | - Alejandro Morales-Bayuelo
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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12
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Ibeji CU, Tolufashe GF, Ntombela T, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling. Tuberculosis (Edinb) 2018; 113:222-230. [PMID: 30514506 DOI: 10.1016/j.tube.2018.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/11/2018] [Accepted: 10/14/2018] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of Tuberculosis. Formation of 3 → 3 crosslinks in the peptidoglycan layer of M. tuberculosis is catalyzed by l,d-transpeptidases. These enzymes can confer resistance against classical β-lactams that inhibit enzymes that generate 4 → 3 peptidoglycan crosslinks. The focus of this study is to investigate the catalytic role of water molecules in the acylation mechanism of the β-lactam ring within two models; 4- and 6-membered ring systems using two-layered our Own N-layer integrated Molecular Mechanics ONIOM (B3LYP/6-311++G(2d,2p): AMBER) model. The obtained thermochemical parameters revealed that the 6-membered ring model best describes the inhibition mechanism of acylation which indicates the role of water in the preference of 6-membered ring reaction pathway. This finding is in accordance with experimental data for the rate-limiting step of cysteine protease with the same class of inhibitor and binding affinity for both inhibitors. As expected, the ΔG# results also reveal that the 6-membered ring reaction pathway is the most favourable. The electrostatic potential (ESP) and the natural bond orbital analysis (NBO) showed stronger interactions in 6-membered ring transition state (TS-6) mechanism involving water in the active site of the enzyme. This study could be helpful in the development of novel antibiotics against l,d-transpeptidase.
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Affiliation(s)
- Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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13
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Khondker A, Malenfant DJ, Dhaliwal AK, Rheinstädter MC. Carbapenems and Lipid Bilayers: Localization, Partitioning, and Energetics. ACS Infect Dis 2018; 4:926-935. [PMID: 29582993 DOI: 10.1021/acsinfecdis.7b00156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbapenems are broad-spectrum antibiotics used today to treat otherwise antibiotic resistant bacteria. As their target transpeptidase is located within the periplasm of the Gram-negative bacteria, they can participate in nonspecific interactions between the inner leaflet of the outer membrane and the outer leaflet of the inner membrane. We, therefore, studied the interaction of the four most clinically relevant carbapenems, namely, imipenem, doripenem, ertapenem, and meropenem, with model phospholipid bilayers made of 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) using molecular dynamics (MD) simulations and X-ray diffraction at low and high concentration of the drugs corresponding to 1 and 8 mol % (with respect to the number of membrane lipids). Membrane solubility was found to decrease from imipenem to doripenem, ertapenem, and finally meropenem. At low concentrations, membrane insertion was found to be a two step process, where the drugs first adsorb to the lipid head groups before inserting through a rotation of the molecule. At higher drug concentrations, the molecules were found to form aggregates in the aqueous phase before making contact with the membranes and spontaneously inserting into the bilayers. Two populations of imipenem were found: in the headgroup at ∼17 Å from the bilayer center and an inserted population at z-values of about 7 Å. Other carbapenems were found to localize in the tail groups with meropenem at ∼10 Å, doripenem at ∼8 Å, and ertapenem at ∼8 Å. The observed membrane solubility of carbapenems can potentially impact the availability of the drug to the target penicillin-binding proteins, potentially affecting their clinical efficacy.
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Affiliation(s)
- Adree Khondker
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Dylan J. Malenfant
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Alexander K. Dhaliwal
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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14
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Fakhar Z, Govender T, Lamichhane G, Maguire GE, Kruger HG, Honarparvar B. Computational model for the acylation step of the β-lactam ring: Potential application for l,d-transpeptidase 2 in mycobacterium tuberculosis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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15
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Bhattacharjee N, Field MJ, Simorre JP, Arthur M, Bougault CM. Hybrid Potential Simulation of the Acylation of Enterococcus faecium l,d-Transpeptidase by Carbapenems. J Phys Chem B 2016; 120:4767-81. [DOI: 10.1021/acs.jpcb.6b02836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicholus Bhattacharjee
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Martin J. Field
- DYNAMO/DYNAMOP,
UMR 5075, Université Grenoble 1, CNRS, CEA, Institut de Biologie
Structurale, 71 Avenue des Martyrs,
CS 10090, 38044 Grenoble Cedex 9, France
| | - Jean-Pierre Simorre
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
| | - Michel Arthur
- Centre de Recherche
des Cordeliers, Equipe 12, UMR S 872, Université Pierre et
Marie Curie-Paris 6, INSERM, Université Paris Descartes, Sorbonne
Paris Cité, 15 rue de l’Ecole
de Médecine, 75006 Paris, France
| | - Catherine M. Bougault
- RMN, UMR 5075,
Université Grenoble 1, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France
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16
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García-Guevara F, Avelar M, Ayala M, Segovia L. Computational Tools Applied to Enzyme Design − a review. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/boca-2015-0009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AbstractThe protein design toolbox has been greatly improved by the addition of enzyme computational simulations. Not only do they warrant a more ambitious and thorough exploration of sequence space, but a much higher number of variants and protein-ligand systems can be analyzed in silico compared to experimental engineering methods. Modern computational tools are being used to redesign and also for de novo generation of enzymes. These approaches are contingent on a deep understanding of the reaction mechanism and the enzyme’s three-dimensional structure coordinates, but the wealth of information produced by these analyses leads to greatly improved or even totally new types of catalysis.
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17
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Kim HS, Im HN, An DR, Yoon JY, Jang JY, Mobashery S, Hesek D, Lee M, Yoo J, Cui M, Choi S, Kim C, Lee NK, Kim SJ, Kim JY, Bang G, Han BW, Lee BI, Yoon HJ, Suh SW. The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase. J Biol Chem 2015; 290:25103-17. [PMID: 26306031 PMCID: PMC4599014 DOI: 10.1074/jbc.m115.658781] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of l,d-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known l,d-transpeptidases. Mass analyses confirm that Csd6 functions only as an l,d-carboxypeptidase and not as an l,d-transpeptidase. The d-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of l,d-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.
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Affiliation(s)
- Hyoun Sook Kim
- From the Departments of Chemistry and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Doo Ri An
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Ji Young Yoon
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | | | - Shahriar Mobashery
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Dusan Hesek
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Mijoon Lee
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jakyung Yoo
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Minghua Cui
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun Choi
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Cheolhee Kim
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Nam Ki Lee
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Soon-Jong Kim
- the Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Jin Young Kim
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Geul Bang
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Il Lee
- the Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea
| | | | - Se Won Suh
- From the Departments of Chemistry and Biophysics and Chemical Biology, College of Natural Sciences, and
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18
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Silva JRA, Bishai WR, Govender T, Lamichhane G, Maguire GEM, Kruger HG, Lameira J, Alves CN. Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2. J Biomol Struct Dyn 2015; 34:304-17. [PMID: 25762064 DOI: 10.1080/07391102.2015.1029000] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-LdtMt2 - residues 120-408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of Mycobacterium tuberculosis. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.
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Affiliation(s)
- José Rogério A Silva
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
| | - William R Bishai
- b Department of Medicine, Division of Infectious Diseases , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Thavendran Govender
- c Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Gyanu Lamichhane
- c Catalysis and Peptide Research Unit, School of Health Sciences , University of KwaZulu-Natal , Durban 4001 , South Africa
| | - Glenn E M Maguire
- d Taskforce to study Resistance Emergence & Antimicrobial Development Technology , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Hendrik G Kruger
- d Taskforce to study Resistance Emergence & Antimicrobial Development Technology , Johns Hopkins University School of Medicine , Baltimore , MD 21205 , USA
| | - Jeronimo Lameira
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
| | - Cláudio N Alves
- a Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais , Universidade Federal do Pará , CP 11101, Belém , PA 66075-110 , Brazil
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19
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Alves CN, Silva JRA, Roitberg AE. Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study. Phys Chem Chem Phys 2015; 17:17790-6. [PMID: 26087682 DOI: 10.1039/c5cp02016f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) enzyme catalyzes the unique redox reaction in the de novo pyrimidine biosynthesis pathway. In this reaction, the oxidation of dihydroorotate (DHO) to orotate (OA) and reduction of the flavin mononucleotide (FMN) cofactor is catalysed by DHOD. The class 2 DHOD, to which the human enzyme belongs, was experimentally shown to follow a stepwise mechanism but the data did not allow the determination of the order of bond-breaking in a stepwise oxidation of DHO. The goal of this study is to understand the reaction mechanism at the molecular level of class 2 DHOD, which may aid in the design of inhibitors that selectively impact the activity of only certain members of the enzyme family. In this paper, the catalytic mechanism of oxidation of DHO to OA in human DHOD was studied using a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) approach and Molecular Dynamics (MD) simulations. The free energy barriers calculated reveal that the mechanism in human DHOD occurs via a stepwise reaction pathway. In the first step, a proton is abstracted from the C5 of DHO to the deprotonated Ser215 side chain. Whereas, in the second step, the transfer of the hydride or hydride equivalent from the C6 of DHO to the N5 of FMN, where free energy barrier calculated by the DFT/MM level is 10.84 kcal mol(-1). Finally, a residual decomposition analysis was carried out in order to elucidate the influence of the catalytic region residues during DHO oxidation.
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Affiliation(s)
- Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil. mail:
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20
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Silva JRA, Roitberg AE, Alves CN. A QM/MM free energy study of the oxidation mechanism of dihydroorotate dehydrogenase (class 1A) from Lactococcus lactis. J Phys Chem B 2015; 119:1468-73. [PMID: 25564307 DOI: 10.1021/jp512860r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) class 1A enzyme catalyzes is the only redox enzyme in the biosynthetic pathway (de novo) of pyrimidines where dihydroorotate (DHO) is oxidized to orotate (OA) coupled to reduction of a flavin mononucleotide (FMN) cofactor. The rupture of two DHO C-H bonds can proceed in a concerted or stepwise way. Herein, the catalytic mechanism of DHOD from Lactococcus lactis involving DHO oxidation (first half-reaction) was described using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach and molecular dynamics simulations. The free energy profile obtained from self-consistent charge-density functional tight binding/molecular mechanics calculations (corrected by DFT/MM) reveals that this occurs with the proton abstraction from DHO C5 to Cys130 deprotonated and DHO H6 is transferred to FMN N5 in a concerted mechanism with a very low barrier of 5.64 kcal/mol. Finally, through a residual decomposition analysis, the residues that have the main influence on the redox reaction were identified.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , Belém, PA 66075-110, Brazil
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21
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Silva JRA, Govender T, Maguire GEM, Kruger HG, Lameira J, Roitberg AE, Alves CN. Simulating the inhibition reaction of Mycobacterium tuberculosisl,d-transpeptidase 2 by carbapenems. Chem Commun (Camb) 2015; 51:12560-2. [DOI: 10.1039/c5cc03202d] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The inactivation mechanism of LDT enzyme from M. tuberculosis by carbapenems is described by QM/MM and PMF analysis
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Affiliation(s)
- José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos
- Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém
- Brazil
| | - Thavendran Govender
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of Kwazulu-Natal
- Durban 4001
- South Africa
| | - Glenn E. M. Maguire
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of Kwazulu-Natal
- Durban 4001
- South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit
- School of Health Sciences
- University of Kwazulu-Natal
- Durban 4001
- South Africa
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos
- Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém
- Brazil
| | | | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos
- Instituto de Ciências Exatas e Naturais
- Universidade Federal do Pará
- Belém
- Brazil
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