1
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Cele ZED, Matshe W, Mdlalose L, Setshedi K, Malatji K, Mkhwanazi NP, Ntombela T, Balogun M. Cationic Chitosan Derivatives for the Inactivation of HIV-1 and SARS-CoV-2 Enveloped Viruses. ACS Omega 2023; 8:31714-31724. [PMID: 37692209 PMCID: PMC10483524 DOI: 10.1021/acsomega.3c02143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023]
Abstract
Cationic chitosan derivatives have been widely studied as potential antimicrobial agents. However, very little is known about their antiviral activity and mode of action against enveloped viruses. We investigated the ability of hydroxypropanoic acid-grafted chitosan (HPA-CS) and N-(2-hydroxypropyl)-3-trimethylammonium chitosan chloride (HTCC) to inactivate enveloped viruses like the human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The membrane-disrupting potential of the chitosan derivatives was initially investigated in a hemolysis assay. At 1.0 mg/mL, about 80% hemolysis was observed for the cationic chitosan derivatives, which was significant when compared to almost no membrane-disrupting activity by the unmodified chitosan. Virus inhibition was evaluated using the luciferase-based antiviral assay against the HIV-1 NL4.3 virus (400 TCID). The IC50 of HPA-CS was 4.109 mg/mL, while the HTCC showed a higher antiviral activity at an IC50 = 0.225 mg/mL. For practical application, the antiviral efficacies of the HTCC-coated and uncoated nonmedical masks were evaluated for SARS- CoV-2 virus capture. The coated masks demonstrated an almost excellent performance with nearly 100% viral inhibition compared to less than 60% inhibition by the uncoated masks. Molecular docking predictions suggest that the HTCC polymers interact with the viral spike protein, blocking the coronavirus interaction with the target host cell's angiotensin-converting enzyme 2 cellular receptors.
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Affiliation(s)
- Zamani E. D. Cele
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - William Matshe
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Lindani Mdlalose
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Katlego Setshedi
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Kanyane Malatji
- Emerging
Research Area Platform, Next Generation Health Cluster, Council for Scientific and Industrial Research, Pretoria, Gauteng 0001, South Africa
| | - Nompumelelo Prudence Mkhwanazi
- College
of Health Science, School of Laboratory Medicine and Medical Science,
HIV Pathogenesis Programme, University of
KwaZulu-Natal, Durban, KwaZulu-Natal 4041 South Africa
| | - Thandokuhle Ntombela
- Faculty
of Science, School of Chemistry, University
of the Witwatersrand, Johannesburg 00000, South Africa
| | - Mohammed Balogun
- Bio-Polymer
Modification and Advanced Therapeutics Laboratory, Centre for Nanostructures
and Advanced Materials, Council for Scientific
and Industrial Research, Pretoria, Gauteng 0001, South Africa
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2
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Dube ZF, Soremekun OS, Ntombela T, Alahmdi MI, Abo-Dya NE, Sidhom PA, Shawky AM, Shibl MF, Ibrahim MA, Soliman ME. Inherent efficacies of pyrazole-based derivatives for cancer therapy: the interface between experiment and in silico. Future Med Chem 2023; 15:1719-1738. [PMID: 37772542 DOI: 10.4155/fmc-2023-0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
There has been an increasing trend in the design of novel pyrazole derivatives for desired biological applications. For a cost-effective strategy, scientists have implemented various computational drug design tools to go hand in hand with experiments for the design and discovery of potentially effective pyrazole-based therapeutics. This review highlights the milestones of pyrazole-containing inhibitors and the use of molecular modeling techniques in conjunction with experimental studies to provide a view of the binding mechanism of these compounds. The review focuses on the established targets that play a key role in cancer therapy, including proteins involved in tubulin polymerization, carbonic anhydrase and tyrosine kinase. Overall, using both experimental and computational methods in drug design represents a promising approach to cancer therapy.
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Affiliation(s)
- Zanele F Dube
- Molecular Bio-Computational & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Opeyemi S Soremekun
- Molecular Bio-Computational & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, South Kensington, London, SW7 2BX, UK
| | - Thandokuhle Ntombela
- Catalysis & Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mohammed Issa Alahmdi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, 71491, Saudi Arabia
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk, Tabuk, 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Egypt
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, 31527, Egypt
| | - Ahmed M Shawky
- Science & Technology Unit, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Mohamed F Shibl
- Renewable Energy Program, Center for Sustainable Development, College of Arts & Sciences, Qatar University, Doha, 2713, Qatar
| | - Mahmoud Aa Ibrahim
- Molecular Bio-Computational & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Mahmoud Es Soliman
- Molecular Bio-Computational & Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
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3
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Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Res 2023; 217:105675. [PMID: 37481039 DOI: 10.1016/j.antiviral.2023.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.
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Affiliation(s)
- Sibusiso B Maseko
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Yasmine Brammerloo
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Adrià Sogues
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Julien Olivet
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | | | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Bazarbachi
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates
| | - Han Remaut
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels Belgium.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium; Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates.
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4
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Nyembe PL, Ntombela T, Makatini MM. Review: Structure-Activity Relationship of Antimicrobial Peptoids. Pharmaceutics 2023; 15:pharmaceutics15051506. [PMID: 37242748 DOI: 10.3390/pharmaceutics15051506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Due to their broad-spectrum activity against Gram-negative and Gram-positive bacteria, natural antimicrobial peptides (AMPs) and their synthetic analogs have emerged as prospective therapies for treating illnesses brought on by multi-drug resistant pathogens. To overcome the limitations of AMPs, such as protease degradation, oligo-N-substituted glycines (peptoids) are a promising alternative. Despite having the same backbone atom sequence as natural peptides, peptoid structures are more stable because, unlike AMP, their functional side chains are attached to the backbone nitrogen (N)-atom rather than the alpha carbon atom. As a result, peptoid structures are less susceptible to proteolysis and enzymatic degradation. The advantages of AMPs, such as hydrophobicity, cationic character, and amphipathicity, are mimicked by peptoids. Furthermore, structure-activity relationship studies (SAR) have shown that tuning the structure of peptoids is a crucial step in developing effective antimicrobials.
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Affiliation(s)
- Priscilla L Nyembe
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Thandokuhle Ntombela
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Maya M Makatini
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa
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5
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Reddy N, Girdhari L, Shungube M, Gouws AC, Peters BK, Rajbongshi KK, Baijnath S, Mdanda S, Ntombela T, Arumugam T, Bester LA, Singh SD, Chuturgoon A, Arvidsson PI, Maguire GEM, Kruger HG, Govender T, Naicker T. Neutralizing Carbapenem Resistance by Co-Administering Meropenem with Novel β-Lactam-Metallo-β-Lactamase Inhibitors. Antibiotics (Basel) 2023; 12:antibiotics12040633. [PMID: 37106995 PMCID: PMC10135050 DOI: 10.3390/antibiotics12040633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
Virulent Enterobacterale strains expressing serine and metallo-β-lactamases (MBL) genes have emerged responsible for conferring resistance to hard-to-treat infectious diseases. One strategy that exists is to develop β-lactamase inhibitors to counter this resistance. Currently, serine β-lactamase inhibitors (SBLIs) are in therapeutic use. However, an urgent global need for clinical metallo-β-lactamase inhibitors (MBLIs) has become dire. To address this problem, this study evaluated BP2, a novel beta-lactam-derived β-lactamase inhibitor, co-administered with meropenem. According to the antimicrobial susceptibility results, BP2 potentiates the synergistic activity of meropenem to a minimum inhibitory concentration (MIC) of ≤1 mg/L. In addition, BP2 is bactericidal over 24 h and safe to administer at the selected concentrations. Enzyme inhibition kinetics showed that BP2 had an apparent inhibitory constant (Kiapp) of 35.3 µM and 30.9 µM against New Delhi Metallo-β-lactamase (NDM-1) and Verona Integron-encoded Metallo-β-lactamase (VIM-2), respectively. BP2 did not interact with glyoxylase II enzyme up to 500 µM, indicating specific (MBL) binding. In a murine infection model, BP2 co-administered with meropenem was efficacious, observed by the >3 log10 reduction in K. pneumoniae NDM cfu/thigh. Given the promising pre-clinical results, BP2 is a suitable candidate for further research and development as an (MBLI).
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Affiliation(s)
- Nakita Reddy
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Letisha Girdhari
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Mbongeni Shungube
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Arnoldus C Gouws
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Byron K Peters
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Kamal K Rajbongshi
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
- School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2020, South Africa
| | - Sipho Mdanda
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A Bester
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sanil D Singh
- Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban 3629, South Africa
| | - Anil Chuturgoon
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Per I Arvidsson
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
- Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, 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, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Department of Chemistry, University of Zululand, Private Bag X1001, KwaDlangezwa 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu-Natal, Durban 4001, South Africa
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6
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Mushebenge AG, Ugbaja SC, Mtambo SE, Ntombela T, Metu JI, Babayemi O, Chima JI, Appiah-Kubi P, Odugbemi AI, Ntuli ML, Khan R, Kumalo HM. Unveiling the Inhibitory Potentials of Peptidomimetic Azanitriles and Pyridyl Esters towards SARS-CoV-2 Main Protease: A Molecular Modelling Investigation. Molecules 2023; 28:molecules28062641. [PMID: 36985614 PMCID: PMC10051727 DOI: 10.3390/molecules28062641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/17/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for COVID-19, which was declared a global pandemic in March 2020 by the World Health Organization (WHO). Since SARS-CoV-2 main protease plays an essential role in the virus’s life cycle, the design of small drug molecules with lower molecular weight has been a promising development targeting its inhibition. Herein, we evaluated the novel peptidomimetic azatripeptide and azatetrapeptide nitriles against SARS-CoV-2 main protease. We employed molecular dynamics (MD) simulations to elucidate the selected compounds’ binding free energy profiles against SARS-CoV-2 and further unveil the residues responsible for the drug-binding properties. Compound 8 exhibited the highest binding free energy of −49.37 ± 0.15 kcal/mol, followed by compound 7 (−39.83 ± 0.19 kcal/mol), while compound 17 showed the lowest binding free energy (−23.54 ± 0.19 kcal/mol). In addition, the absorption, distribution, metabolism, and excretion (ADME) assessment was performed and revealed that only compound 17 met the drug-likeness parameters and exhibited high pharmacokinetics to inhibit CYP1A2, CYP2C19, and CYP2C9 with better absorption potential and blood-brain barrier permeability (BBB) index. The additional intermolecular evaluations suggested compound 8 as a promising drug candidate for inhibiting SARS-CoV-2 Mpro. The substitution of isopropane in compound 7 with an aromatic benzene ring in compound 8 significantly enhanced the drug’s ability to bind better at the active site of the SARS-CoV-2 Mpro.
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Affiliation(s)
- Aganze G. Mushebenge
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Samuel C. Ugbaja
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
- Correspondence: (S.C.U.); (H.M.K.)
| | - Sphamandla E. Mtambo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Pharmaceutical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Joy I. Metu
- National Institute for Nigerian Languages, Aba 453106, Nigeria;
| | - Oludotun Babayemi
- Cloneshouse Nigeria, 6th Floor, Left Wing, NICON Plaza, Plot 242, Muhammadu Buhari Way, Central Business District, Abuja 900103, Nigeria;
| | - Joy I. Chima
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Patrick Appiah-Kubi
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Adeshina I. Odugbemi
- South African National Bioinformatics Institute, Faculty of Natural Sciences, University of the Western Cape, Cape Town 7535, South Africa;
| | - Mthobisi L. Ntuli
- Department of Mathematics, Faculty of Applied Science, Durban University of Technology, Durban 4000, South Africa;
| | - Rene Khan
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
| | - Hezekiel M. Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa; (A.G.M.); (S.E.M.); (J.I.C.); (P.A.-K.); (R.K.)
- Correspondence: (S.C.U.); (H.M.K.)
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7
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Peters BK, Reddy N, Shungube M, Girdhari L, Baijnath S, Mdanda S, Chetty L, Ntombela T, Arumugam T, Bester LA, Singh SD, Chuturgoon A, Arvidsson PI, Maguire GEM, Kruger HG, Naicker T, Govender T. In Vitro and In Vivo Development of a β-Lactam-Metallo-β-Lactamase Inhibitor: Targeting Carbapenem-Resistant Enterobacterales. ACS Infect Dis 2023; 9:486-496. [PMID: 36786013 PMCID: PMC10012271 DOI: 10.1021/acsinfecdis.2c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
β-lactams are the most prescribed class of antibiotics due to their potent, broad-spectrum antimicrobial activities. However, alarming rates of antimicrobial resistance now threaten the clinical relevance of these drugs, especially for the carbapenem-resistant Enterobacterales expressing metallo-β-lactamases (MBLs). Antimicrobial agents that specifically target these enzymes to restore the efficacy of last resort β-lactam drugs, that is, carbapenems, are therefore desperately needed. Herein, we present a cyclic zinc chelator covalently attached to a β-lactam scaffold (cephalosporin), that is, BP1. Observations from in vitro assays (with seven MBL expressing bacteria from different geographies) have indicated that BP1 restored the efficacy of meropenem to ≤ 0.5 mg/L, with sterilizing activity occurring from 8 h postinoculation. Furthermore, BP1 was nontoxic against human hepatocarcinoma cells (IC50 > 1000 mg/L) and exhibited a potency of (Kiapp) 24.8 and 97.4 μM against Verona integron-encoded MBL (VIM-2) and New Delhi metallo β-lactamase (NDM-1), respectively. There was no inhibition observed from BP1 with the human zinc-containing enzyme glyoxylase II up to 500 μM. Preliminary molecular docking of BP1 with NDM-1 and VIM-2 sheds light on BP1's mode of action. In Klebsiella pneumoniae NDM infected mice, BP1 coadministered with meropenem was efficacious in reducing the bacterial load by >3 log10 units' postinfection. The findings herein propose a favorable therapeutic combination strategy that restores the activity of the carbapenem antibiotic class and complements the few MBL inhibitors under development, with the ultimate goal of curbing antimicrobial resistance.
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Affiliation(s)
- Byron K Peters
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Nakita Reddy
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mbongeni Shungube
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Letisha Girdhari
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Sooraj Baijnath
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa.,School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng 2193, South Africa
| | - Sipho Mdanda
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Lloyd Chetty
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Linda A Bester
- Biomedical Research Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sanil D Singh
- Department of Pharmaceutical Science, University of KwaZulu-Natal, Westville Campus, Durban 3629, South Africa
| | - Anil Chuturgoon
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Per I Arvidsson
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa.,Science for Life Laboratory, Drug Discovery & Development Platform & Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, 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, University of KwaZulu Natal, Durban 4001, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Department of Chemistry, University of Zululand, Private Bag X1001, KwaDlangezwa, Empangeni 3886, South Africa
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8
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- 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.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical 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
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- 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.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ntombela T, Fakhar Z, Ibeji CU, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. Molecular insight on the non-covalent interactions between carbapenems and L,D-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study. J Comput Aided Mol Des 2018; 32:687-701. [PMID: 29845435 DOI: 10.1007/s10822-018-0121-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/14/2018] [Indexed: 12/01/2022]
Abstract
Tuberculosis remains a dreadful disease that has claimed many human lives worldwide and elimination of the causative agent Mycobacterium tuberculosis also remains elusive. Multidrug-resistant TB is rapidly increasing worldwide; therefore, there is an urgent need for improving the current antibiotics and novel drug targets to successfully curb the TB burden. L,D-Transpeptidase 2 is an essential protein in Mtb that is responsible for virulence and growth during the chronic stage of the disease. Both D,D- and L,D-transpeptidases are inhibited concurrently to eradicate the bacterium. It was recently discovered that classic penicillins only inhibit D,D-transpeptidases, while L,D-transpeptidases are blocked by carbapenems. This has contributed to drug resistance and persistence of tuberculosis. Herein, a hybrid two-layered ONIOM (B3LYP/6-31G+(d): AMBER) model was used to extensively investigate the binding interactions of LdtMt2 complexed with four carbapenems (biapenem, imipenem, meropenem, and tebipenem) to ascertain molecular insight of the drug-enzyme complexation event. In the studied complexes, the carbapenems together with catalytic triad active site residues of LdtMt2 (His187, Ser188 and Cys205) were treated at with QM [B3LYP/6-31+G(d)], while the remaining part of the complexes were treated at MM level (AMBER force field). The resulting Gibbs free energy (ΔG), enthalpy (ΔH) and entropy (ΔS) for all complexes showed that the carbapenems exhibit reasonable binding interactions towards LdtMt2. Increasing the number of amino acid residues that form hydrogen bond interactions in the QM layer showed significant impact in binding interaction energy differences and the stabilities of the carbapenems inside the active pocket of LdtMt2. The theoretical binding free energies obtained in this study reflect the same trend of the experimental observations. The electrostatic, hydrogen bonding and Van der Waals interactions between the carbapenems and LdtMt2 were also assessed. To further examine the nature of intermolecular interactions for carbapenem-LdtMt2 complexes, AIM and NBO analysis were performed for the QM region (carbapenems and the active residues of LdtMt2) of the complexes. These analyses revealed that the hydrogen bond interactions and charge transfer from the bonding to anti-bonding orbitals between catalytic residues of the enzyme and selected ligands enhances the binding and stability of carbapenem-LdtMt2 complexes. The two-layered ONIOM (B3LYP/6-31+G(d): Amber) model was used to evaluate the efficacy of FDA approved carbapenems antibiotics towards LdtMt2.
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Affiliation(s)
- Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Zeynab Fakhar
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield 0002, Pretoria, South Africa
| | - Collins U Ibeji
- 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
| | - Gyanu Lamichhane
- Division of Infectious Diseases, School of Medicine, Center of Tuberculosis Research, 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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