1
|
Peng X, Zeng Z, Hassan S, Xue Y. The potential of marine natural Products: Recent Advances in the discovery of Anti-Tuberculosis agents. Bioorg Chem 2024; 151:107699. [PMID: 39128242 DOI: 10.1016/j.bioorg.2024.107699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Tuberculosis (TB) is an infectious airborne disease caused by Mycobacterium tuberculosis. Since the 1990 s, many countries have made significant progress in reducing the incidence of TB and associated mortality by improving health services and strengthening surveillance systems. Nevertheless, due to the emergence of multidrug-resistant TB (MDR-TB), alongside extensively drug-resistant TB (XDR-TB) and TB-HIV co-infection, TB remains one of the lead causes of death arising from infectious disease worldwide, especially in developing countries and disadvantaged populations. Marine natural products (MNPs) have received a large amount of attention in recent years as a source of pharmaceutical constituents and lead compounds, and are expected to offer significant resources and potential in the fields of drug development and biotechnology in the years to come. This review summarizes 169 marine natural products and their synthetic derivatives displaying anti-TB activity from 2013 to the present, including their structures, sources and functions. Partial synthetic information and structure-activity relationships (SARs) are also included.
Collapse
Affiliation(s)
- Xinyu Peng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Ziqian Zeng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Said Hassan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24540, Pakistan
| | - Yongbo Xue
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China.
| |
Collapse
|
2
|
Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
Collapse
Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
| |
Collapse
|
3
|
Explicit molecular dynamics simulation studies to discover novel natural compound analogues as Mycobacterium tuberculosis inhibitors. Heliyon 2023; 9:e13324. [PMID: 36816262 PMCID: PMC9932657 DOI: 10.1016/j.heliyon.2023.e13324] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) in one of the dreadful diseases present globally. This is caused by Mycobacterium tuberculosis. Mycobacterium tuberculosis dethiobiotin synthetase (MtDTBS) is an essential enzyme in biotin biosynthesis and is an ideal target to design and develop novel inhibitors. In order to effectively combat this disease six natural compound (butein) analogues were subjected to molecular docking to determine their binding mode and the binding affinities. The resultant complex structures were subjected to 500 ns simulation run to estimate their binding stabilities using GROMACS. The molecular dynamics simulation studies provided essential evidence that the systems were stable during the progression of 500 ns simulation run. The root mean square deviation (RMSD) of all the systems was found to be below 0.3 nm stating that the systems are well converged. The radius of gyration (Rg) profiles indicated that the systems were highly compact without any major fluctuations. The principle component analysis (PCA) and Gibbs energy landscape studies have revealed that the comp3, comp5 and comp11 systems navigated marginally through the PC2. The intermolecular interactions have further demonstrated that all the compounds have displayed key residue interactions, firmly holding the ligands at the binding pocket. The residue Lys37 was found consistently to interact with all the ligands highlighting its potential role in inhibiting the MtDTBS. Our investigation further put forth two novel compounds (comp10 and comp11) as putative antituberculosis agents. Collectively, we propose six compounds has plausible inhibitors to curtail TB and further can act as scaffolds in designing new compounds.
Collapse
|
4
|
Larkins-Ford J, Aldridge BB. Advances in the design of combination therapies for the treatment of tuberculosis. Expert Opin Drug Discov 2023; 18:83-97. [PMID: 36538813 PMCID: PMC9892364 DOI: 10.1080/17460441.2023.2157811] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Tuberculosis requires lengthy multi-drug therapy. Mycobacterium tuberculosis occupies different tissue compartments during infection, making drug access and susceptibility patterns variable. Antibiotic combinations are needed to ensure each compartment of infection is reached with effective drug treatment. Despite drug combinations' role in treating tuberculosis, the design of such combinations has been tackled relatively late in the drug development process, limiting the number of drug combinations tested. In recent years, there has been significant progress using in vitro, in vivo, and computational methodologies to interrogate combination drug effects. AREAS COVERED This review discusses the advances in these methodologies and how they may be used in conjunction with new successful clinical trials of novel drug combinations to design optimized combination therapies for tuberculosis. Literature searches for approaches and experimental models used to evaluate drug combination effects were undertaken. EXPERT OPINION We are entering an era richer in combination drug effect and pharmacokinetic/pharmacodynamic data, genetic tools, and outcome measurement types. Application of computational modeling approaches that integrate these data and produce predictive models of clinical outcomes may enable the field to generate novel, effective multidrug therapies using existing and new drug combination backbones.
Collapse
Affiliation(s)
- Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Current address: MarvelBiome Inc, Woburn, MA, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA
| |
Collapse
|
5
|
Si A, Landgraf AD, Geden S, Sucheck SJ, Rohde KH. Synthesis and Evaluation of Marine Natural Product-Inspired Meroterpenoids with Selective Activity toward Dormant Mycobacterium tuberculosis. ACS OMEGA 2022; 7:23487-23496. [PMID: 35847331 PMCID: PMC9281309 DOI: 10.1021/acsomega.2c01887] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tuberculosis is a disease caused primarily by the organism Mycobacterium tuberculosis (Mtb), which claims about 1.5 million lives every year. A challenge that impedes the elimination of this pathogen is the ability of Mtb to remain dormant after primary infection, thus creating a reservoir for the disease in the population that reactivates under more ideal conditions. A better understanding of the physiology of dormant Mtb and therapeutics able to kill these phenotypically tolerant bacilli will be critical for completely eradicating Mtb. Our groups are focusing on characterizing the activity of derivatives of the marine natural product (+)-puupehenone (1). Recently, the Rohde group reported that puupehedione (2) and 15-α-methoxypuupehenol (3) exhibit enhanced activity in an in vitro multi-stress dormancy model of Mtb. To optimize the antimycobacterial activity of these terpenoids, novel 15-α-methoxy- and 15-α-acetoxy-puupehenol esters were prepared from (+)-puupehenone (1) accessed through a (+)-sclareolide-derived β-hydroxyl aldehyde. For added diversity, various congeners related to (1) were also prepared from a common borono-sclareolide donor, which resulted in the synthesis of epi-puupehenol and the natural products (+)-chromazonarol and (+)-yahazunol. In total, we generated a library of 24 compounds, of which 14 were found to be active against Mtb, and the most active compounds retained the enhanced activity against dormant Mtb seen in the parent compound. Several of the 15-α-methoxy- and 15-α-acetoxy-puupehenol esters possessed potent activity against actively dividing and dormant Mtb. Intriguingly, the closely related triisobutyl derivative 16 showed similar activity to 1 in actively dividing Mtb but lost about 178-fold activity against dormant Mtb. However, the monopivaloyl compound 13 showed a modest 3- to 4-fold loss in activity in both actively dividing and dormant Mtb relative to the activity of 1 revealing the importance of the free OH at C19 supporting the potential role of quinone methide formation as critical for activity in dormant Mtb. Elucidating important structure-activity relationships and the mechanism of action of this natural product-inspired chemical series may yield insights into vulnerable drug targets in dormant bacilli and new therapeutics to more effectively target dormant Mtb.
Collapse
Affiliation(s)
- Anshupriya Si
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Alexander D. Landgraf
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Sandra Geden
- Division
of Immunity and Pathogenesis, Burnett School of Biomedical Sciences,
College of Medicine, University of Central
Florida, Orlando, Florida 32827, United
States
| | - Steven J. Sucheck
- Department
of Chemistry and Biochemistry, University
of Toledo, 2801 West Bancroft Street, Toledo, Ohio 43606, United
States
| | - Kyle H. Rohde
- Division
of Immunity and Pathogenesis, Burnett School of Biomedical Sciences,
College of Medicine, University of Central
Florida, Orlando, Florida 32827, United
States
| |
Collapse
|
6
|
Rahman MM, Islam MR, Shohag S, Hossain ME, Shah M, Shuvo SK, Khan H, Chowdhury MAR, Bulbul IJ, Hossain MS, Sultana S, Ahmed M, Akhtar MF, Saleem A, Rahman MH. Multifaceted role of natural sources for COVID-19 pandemic as marine drugs. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:46527-46550. [PMID: 35507224 PMCID: PMC9065247 DOI: 10.1007/s11356-022-20328-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/14/2022] [Indexed: 05/05/2023]
Abstract
COVID-19, which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has quickly spread over the world, posing a global health concern. The ongoing epidemic has necessitated the development of novel drugs and potential therapies for patients infected with SARS-CoV-2. Advances in vaccination and medication development, no preventative vaccinations, or viable therapeutics against SARS-CoV-2 infection have been developed to date. As a result, additional research is needed in order to find a long-term solution to this devastating condition. Clinical studies are being conducted to determine the efficacy of bioactive compounds retrieved or synthesized from marine species starting material. The present study focuses on the anti-SARS-CoV-2 potential of marine-derived phytochemicals, which has been investigated utilizing in in silico, in vitro, and in vivo models to determine their effectiveness. Marine-derived biologically active substances, such as flavonoids, tannins, alkaloids, terpenoids, peptides, lectins, polysaccharides, and lipids, can affect SARS-CoV-2 during the viral particle's penetration and entry into the cell, replication of the viral nucleic acid, and virion release from the cell; they can also act on the host's cellular targets. COVID-19 has been proven to be resistant to several contaminants produced from marine resources. This paper gives an overview and summary of the various marine resources as marine drugs and their potential for treating SARS-CoV-2. We discussed at numerous natural compounds as marine drugs generated from natural sources for treating COVID-19 and controlling the current pandemic scenario.
Collapse
Affiliation(s)
- Md Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Md Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Sheikh Shohag
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj-8100, Gopalganj, Bangladesh
| | - Md Emon Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Muddaser Shah
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Shakil Khan Shuvo
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Hosneara Khan
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | | | - Israt Jahan Bulbul
- Department of Pharmacy, Southeast University, Banani, Dhaka, 1213, Bangladesh
| | - Md Sarowar Hossain
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Sharifa Sultana
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Muhammad Furqan Akhtar
- Riphah Institute of Pharmaceutical Sciences, Riphah International University Lahore Campus, Lahore, Pakistan
| | - Ammara Saleem
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Md Habibur Rahman
- Department of Pharmacy, Southeast University, Banani, Dhaka, 1213, Bangladesh.
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju, 26426, Korea.
| |
Collapse
|
7
|
Design, synthesis and antibacterial activity against pathogenic mycobacteria of conjugated hydroxamic acids, hydrazides and O-alkyl/O-acyl protected hydroxamic derivatives. Bioorg Med Chem Lett 2022; 64:128692. [PMID: 35307568 DOI: 10.1016/j.bmcl.2022.128692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/04/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022]
Abstract
With the aim to discover new antituberculous molecules, three novel series of 23 hydroxamic acids, 13 hydrazides, and 9O-alkyl/O-acyl protected hydroxamic acid derivatives have been synthesized, and fully characterized by spectral 1H NMR, 13C NMR, HRMS) analysis. These compounds were further biologically screened for their in vitro antibacterial activities against three pathogenic mycobacteria - M. abscessus S and R, M. marinum, and M. tuberculosis - as well as for their toxicity towards murine macrophages by the resazurin microtiter assay (REMA). Among the 45 derivatives, 17 compounds (3 hydroxamic acids, 9 hydrazides, and 5O-alkyl/O-acyl protected hydroxamic acids) were nontoxic against murine macrophages. When tested for their antibacterial activity, hydroxamic acid 9 h was found to be the most potent inhibitor against M. abscessus S and R only. Regarding hydrazide series, only 7h was active against M. abscessus R, M. marinum and M. tuberculosis; while the O-acyl protected hydroxamic acid derivatives 14d and 15d displayed promising antibacterial activity against both M. marinum and M. tuberculosis. Since such hydroxamic- and hydrazide-chelating groups have been reported to impair the activity of the peptide deformylase, in silico molecular docking studies in M. tuberculosis peptide deformylase enzyme active site were further performed with 7h in order to predict the possible interaction mode and binding energy of this molecule at the molecular level.
Collapse
|
8
|
Bone Relat RM, Winder PL, Bowden GD, Guzmán EA, Peterson TA, Pomponi SA, Roberts JC, Wright AE, O’Connor RM. High-Throughput Screening of a Marine Compound Library Identifies Anti-Cryptosporidium Activity of Leiodolide A. Mar Drugs 2022; 20:md20040240. [PMID: 35447913 PMCID: PMC9026894 DOI: 10.3390/md20040240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Cryptosporidium sp. are apicomplexan parasites that cause significant morbidity and possible mortality in humans and valuable livestock. There are no drugs on the market that are effective in the population most severely affected by this parasite. This study is the first high-throughput screen for potent anti-Cryptosporidium natural products sourced from a unique marine compound library. The Harbor Branch Oceanographic Institute at Florida Atlantic University has a collection of diverse marine organisms some of which have been subjected to medium pressure liquid chromatography to create an enriched fraction library. Numerous active compounds have been discovered from this library, but it has not been tested against Cryptosporidium parvum. A high-throughput in vitro growth inhibition assay was used to test 3764 fractions in the library, leading to the identification of 23 fractions that potently inhibited the growth of Cryptosporidium parvum. Bioassay guided fractionation of active fractions from a deep-sea sponge, Leiodermatium sp., resulted in the purification of leiodolide A, the major active compound in the organism. Leiodolide A displayed specific anti-Cryptosporidium activity at a half maximal effective concentration of 103.5 nM with selectivity indexes (SI) of 45.1, 11.9, 19.6 and 14.3 for human ileocecal colorectal adenocarcinoma cells (HCT-8), human hepatocellular carcinoma cells (Hep G2), human neuroblastoma cells (SH-SY5Y) and green monkey kidney cells (Vero), respectively. The unique structure of leiodolide A provides a valuable drug scaffold on which to develop new anti-Cryptosporidium compounds and supports the importance of screening natural product libraries for new chemical scaffolds.
Collapse
Affiliation(s)
- Rachel M. Bone Relat
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, 100 Dairy Rd, Pullman, WA 99164, USA; (R.M.B.R.); (G.D.B.)
| | - Priscilla L. Winder
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
| | - Gregory D. Bowden
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, 100 Dairy Rd, Pullman, WA 99164, USA; (R.M.B.R.); (G.D.B.)
| | - Esther A. Guzmán
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
| | - Tara A. Peterson
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
| | - Jill C. Roberts
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
| | - Amy E. Wright
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (P.L.W.); (E.A.G.); (T.A.P.); (S.A.P.); (J.C.R.)
- Correspondence: (A.E.W.); (R.M.O.)
| | - Roberta M. O’Connor
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, 100 Dairy Rd, Pullman, WA 99164, USA; (R.M.B.R.); (G.D.B.)
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 1971 Commonwealth Ave, St Paul, MN 55108, USA
- Correspondence: (A.E.W.); (R.M.O.)
| |
Collapse
|
9
|
Gupta R, Al-Kharji NMSA, Alqurafi MA, Nguyen TQ, Chai W, Quan P, Malhotra R, Simcox BS, Mortimer P, Brammer Basta LA, Rohde KH, Buynak JD. Atypically Modified Carbapenem Antibiotics Display Improved Antimycobacterial Activity in the Absence of β-Lactamase Inhibitors. ACS Infect Dis 2021; 7:2425-2436. [PMID: 34191496 PMCID: PMC8369493 DOI: 10.1021/acsinfecdis.1c00185] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Commercial carbapenem
antibiotics are being used to treat multidrug
resistant (MDR) and extensively drug resistant (XDR) tuberculosis.
Like other β-lactams, carbapenems are irreversible inhibitors
of serine d,d-transpeptidases involved in peptidoglycan biosynthesis.
In addition to d,d-transpeptidases, mycobacteria also utilize
nonhomologous cysteine l,d-transpeptidases (Ldts) to cross-link
the stem peptides of peptidoglycan, and carbapenems form long-lived
acyl-enzymes with Ldts. Commercial carbapenems are C2 modifications
of a common scaffold. This study describes the synthesis of a series
of atypical, C5α modifications of the carbapenem scaffold, microbiological
evaluation against Mycobacterium tuberculosis (Mtb) and the nontuberculous mycobacterial species, Mycobacterium abscessus (Mab), as well
as acylation of an important mycobacterial target Ldt, LdtMt2. In vitro evaluation of these C5α-modified
carbapenems revealed compounds with standalone (i.e., in the absence of a β-lactamase inhibitor) minimum inhibitory
concentrations (MICs) superior to meropenem-clavulanate for Mtb, and meropenem-avibactam for Mab. Time-kill
kinetics assays showed better killing (2–4 log decrease) of Mtb and Mab with lower concentrations of
compound 10a as compared to meropenem. Although susceptibility
of clinical isolates to meropenem varied by nearly 100-fold, 10a maintained excellent activity against all Mtb and Mab strains. High resolution mass spectrometry
revealed that 10a acylates LdtMt2 at a rate
comparable to meropenem, but subsequently undergoes an unprecedented
carbapenem fragmentation, leading to an acyl-enzyme with mass of Δm = +86 Da. Rationale for the divergence of the nonhydrolytic
fragmentation of the LdtMt2 acyl-enzymes is proposed. The
observed activity illustrates the potential of novel atypical carbapenems
as prospective candidates for treatment of Mtb and Mab infections.
Collapse
Affiliation(s)
- Rashmi Gupta
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | | | - Maha A. Alqurafi
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Thu Q. Nguyen
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Weirui Chai
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Pojun Quan
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Riya Malhotra
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Breven S. Simcox
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Phil Mortimer
- Department of Chemistry, Mass Spectrometry Facility, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Leighanne A. Brammer Basta
- Chemistry Department, United States Naval Academy, 572M Holloway Road, Annapolis, Maryland 21402, United States
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| |
Collapse
|
10
|
Khan MT, Ali A, Wang Q, Irfan M, Khan A, Zeb MT, Zhang YJ, Chinnasamy S, Wei DQ. Marine natural compounds as potents inhibitors against the main protease of SARS-CoV-2-a molecular dynamic study. J Biomol Struct Dyn 2021. [PMID: 32410504 DOI: 10.1080/0739110220201769733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded RNA (ssRNA) virus, responsible for severe acute respiratory disease (COVID-19). A large number of natural compounds are under trial for screening compounds, possessing potential inhibitory effect against the viral infection. Keeping in view the importance of marine compounds in antiviral activity, we investigated the potency of some marine natural products to target SARS-CoV-2 main protease (Mpro) (PDB ID 6MO3). The crystallographic structure of Mpro in an apo form was retrieved from Protein Data Bank and marine compounds from PubChem. These structures were prepared for docking and the complex with good docking score was subjected to molecular dynamic (MD) simulations for a period of 100 ns. To measure the stability, flexibility, and average distance between the target and compounds, root mean square deviations (RMSD), root mean square fluctuation (RMSF), and the distance matrix were calculated. Among five marine compounds, C-1 (PubChem CID 11170714) exhibited good activity, interacting with the active site and surrounding residues, forming many hydrogen and hydrophobic interactions. The C-1 also attained a stable dynamic behavior, and the average distance between compound and target remains constant. In conclusion, marine natural compounds may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
Collapse
Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Pakistan
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Qiankun Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Muhammad Tariq Zeb
- Senior Research Officer, In-charge Genomic Laboratory, Veterinary Research Institute, Peshawar, Peshawar, Pakistan
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, China
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, China Shanghai
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| |
Collapse
|
11
|
The Marine Natural Product Furospinulosin 1 Induces Apoptosis in MDA-MB-231 Triple Negative Breast Cancer Cell Spheroids, But Not in Cells Grown Traditionally with Longer Treatment. Mar Drugs 2021; 19:md19050249. [PMID: 33924764 PMCID: PMC8145321 DOI: 10.3390/md19050249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer cells grown in spheroid conditions interact with each other and the extracellular matrix, providing a better representation of the in vivo environment than two-dimensional cultures and are a more clinically relevant model. A discrete screening of genetically diverse marine samples in the spheroid assay led to the identification of a novel activity for the known compound furospinulosin 1. This compound shows activity against MDA-MB-231 triple negative breast cancer cells grown as spheroids and treated for 24 or 48 h. No cytotoxicity was seen in traditional two-dimensional adherent cultures treated for a longer time (72 h). A reverse phase protein array (RPPA) confirmed the limited activity of the compound in cells grown traditionally and revealed changes in protein expression when cells are grown as spheroids that are associated with better clinical prognosis. Analysis of the RPPA data through the Broad institute’s connectivity map suggested the hypothesis that furospinulosin 1 functions as an MEK inhibitor. Analysis of the RPPA data through STRING supports the apoptosis observed. The selectivity exhibited by furospinulosin 1 for triple negative breast cancer cells only when grown as spheroids makes it an interesting compound with strong therapeutic potential that merits further study.
Collapse
|
12
|
Wright AE, Collins JE, Roberts B, Roberts JC, Winder PL, Reed JK, Diaz MC, Pomponi SA, Chakrabarti D. Antiplasmodial Compounds from Deep-Water Marine Invertebrates. Mar Drugs 2021; 19:md19040179. [PMID: 33805935 PMCID: PMC8064351 DOI: 10.3390/md19040179] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 01/03/2023] Open
Abstract
Novel drug leads for malaria therapy are urgently needed because of the widespread emergence of resistance to all available drugs. Screening of the Harbor Branch enriched fraction library against the Plasmodium falciparum chloroquine-resistant strain (Dd2) followed by bioassay-guided fractionation led to the identification of two potent antiplasmodials; a novel diterpene designated as bebrycin A (1) and the known C21 degraded terpene nitenin (2). A SYBR Green I assay was used to establish a Dd2 EC50 of 1.08 ± 0.21 and 0.29 ± 0.02 µM for bebrycin A and nitenin, respectively. Further analysis was then performed to assess the stage specificity of the inhibitors antiplasmodial effects on the Dd2 intraerythrocytic life cycle. Exposure to bebrycin A was found to block parasite maturation at the schizont stage if added any time prior to late schizogony at 42 hours post invasion, (HPI). In contrast, early life cycle exposure to nitenin (prior to 18 HPI) was identified as crucial to parasite inhibition, suggesting nitenin may target the maturation of the parasite during the transition from ring to early trophozoite (6–18 HPI), a novel property among known antimalarials.
Collapse
Affiliation(s)
- Amy E. Wright
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
- Correspondence: (A.E.W.); (D.C.); Tel.: +1-772-242-2459 (A.E.W.); +1-407-882-2256 (D.C.)
| | - Jennifer E. Collins
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA; (J.E.C.); (B.R.)
| | - Bracken Roberts
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA; (J.E.C.); (B.R.)
| | - Jill C. Roberts
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
| | - Priscilla L. Winder
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
| | - John K. Reed
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
| | - Maria Cristina Diaz
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US Highway 1 North, Fort Pierce, FL 34946, USA; (J.C.R.); (P.L.W.); (J.K.R.); (M.C.D.); (S.A.P.)
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32826, USA; (J.E.C.); (B.R.)
- Correspondence: (A.E.W.); (D.C.); Tel.: +1-772-242-2459 (A.E.W.); +1-407-882-2256 (D.C.)
| |
Collapse
|
13
|
Mayer AMS, Guerrero AJ, Rodríguez AD, Taglialatela-Scafati O, Nakamura F, Fusetani N. Marine Pharmacology in 2016-2017: Marine Compounds with Antibacterial, Antidiabetic, Antifungal, Anti-Inflammatory, Antiprotozoal, Antituberculosis and Antiviral Activities; Affecting the Immune and Nervous Systems, and Other Miscellaneous Mechanisms of Action. Mar Drugs 2021; 19:49. [PMID: 33494402 PMCID: PMC7910995 DOI: 10.3390/md19020049] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
The review of the 2016-2017 marine pharmacology literature was prepared in a manner similar as the 10 prior reviews of this series. Preclinical marine pharmacology research during 2016-2017 assessed 313 marine compounds with novel pharmacology reported by a growing number of investigators from 54 countries. The peer-reviewed literature reported antibacterial, antifungal, antiprotozoal, antituberculosis, and antiviral activities for 123 marine natural products, 111 marine compounds with antidiabetic and anti-inflammatory activities as well as affecting the immune and nervous system, while in contrast 79 marine compounds displayed miscellaneous mechanisms of action which upon further investigation may contribute to several pharmacological classes. Therefore, in 2016-2017, the preclinical marine natural product pharmacology pipeline generated both novel pharmacology as well as potentially new lead compounds for the growing clinical marine pharmaceutical pipeline, and thus sustained with its contributions the global research for novel and effective therapeutic strategies for multiple disease categories.
Collapse
Affiliation(s)
- Alejandro M. S. Mayer
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Aimee J. Guerrero
- Department of Pharmacology, College of Graduate Studies, Midwestern University, 555 31st Street, Downers Grove, IL 60515, USA;
| | - Abimael D. Rodríguez
- Molecular Sciences Research Center, University of Puerto Rico, 1390 Ponce de León Avenue, San Juan, PR 00926, USA;
| | | | - Fumiaki Nakamura
- Department of Chemistry and Biochemistry, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan;
| | | |
Collapse
|
14
|
Giacalone D, Huang L, Tan S. Exploiting Fluorescent Proteins to Understand Mycobacterium tuberculosis Biology. Methods Mol Biol 2021; 2314:365-383. [PMID: 34235663 PMCID: PMC8381720 DOI: 10.1007/978-1-0716-1460-0_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The utility of fluorescent proteins in bacterial research has long been appreciated, with extensive use in the Mycobacterium tuberculosis field. In more recent years, a new generation of fluorescent tools has been developed for use in M. tuberculosis research. These new fluorescent reporters exploit the immense genetic and transcriptional knowledge now available, and enable the use of the bacteria as direct reporters of the local environment during infection, as well as provide insight into bacterial replication status in situ. Here we describe methods for the construction of such fluorescent reporter M. tuberculosis strains, and their use in combination with confocal microscopy and flow cytometry approaches for single bacterium-level analyses of M. tuberculosis physiology and M. tuberculosis-host interactions.
Collapse
Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Lu Huang
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.
| |
Collapse
|
15
|
Zaporozhets TS, Besednova NN. Biologically active compounds from marine organisms in the strategies for combating coronaviruses. AIMS Microbiol 2020; 6:470-494. [PMID: 33364539 PMCID: PMC7755586 DOI: 10.3934/microbiol.2020028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022] Open
Abstract
Despite the progress made in immunization and drug development, so far there are no prophylactic vaccines and effective therapies for many viral infections, including infections caused by coronaviruses. In this regard, the search for new antiviral substances continues to be relevant, and the enormous potential of marine resources are a stimulus for the study of marine compounds with antiviral activity in experiments and clinical trials. The highly pathogenic human coronaviruses-severe acute respiratory syndrome-related coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) remain a serious threat to human health. In this review, the authors hope to bring the attention of researchers to the use of biologically active substances of marine origin as potential broad-spectrum antiviral agents targeting common cellular pathways and various stages of the life cycle of different viruses, including coronaviruses. The review has been compiled using references from major databases such as Web of Science, PubMed, Scopus, Elsevier, Springer and Google Scholar (up to June 2020) and keywords such as 'coronaviruses', 'marine organisms', 'biologically active substances', 'antiviral drugs', 'SARS-CoV', 'MERS-CoV', 'SARS-CoV-2', '3CLpro', 'TMPRSS2', 'ACE2'. After obtaining all reports from the databases, the papers were carefully analysed in order to find data related to the topic of this review (98 references). Biologically active substances of marine origin, such as flavonoids, phlorotannins, alkaloids, terpenoids, peptides, lectins, polysaccharides, lipids and others substances, can affect coronaviruses at the stages of penetration and entry of the viral particle into the cell, replication of the viral nucleic acid and release of the virion from the cell; they also can act on the host's cellular targets. These natural compounds could be a vital resource in the fight against coronaviruses.
Collapse
Affiliation(s)
- Tatyana S. Zaporozhets
- Immunology Laboratory, Somov Institute of Epidemiology and Microbiology, Vladivostok, Russian Federation
| | | |
Collapse
|
16
|
Madani A, Mallick I, Guy A, Crauste C, Durand T, Fourquet P, Audebert S, Camoin L, Canaan S, Cavalier JF. Dissecting the antibacterial activity of oxadiazolone-core derivatives against Mycobacterium abscessus. PLoS One 2020; 15:e0238178. [PMID: 32946441 PMCID: PMC7500638 DOI: 10.1371/journal.pone.0238178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/12/2020] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium abscessus (M. abscessus), a rapidly growing mycobacterium, is an emergent opportunistic pathogen responsible for chronic bronchopulmonary infections in individuals with respiratory diseases such as cystic fibrosis. Most treatments of M. abscessus pulmonary infections are poorly effective due to the intrinsic resistance of this bacteria against a broad range of antibiotics including anti-tuberculosis agents. Consequently, the number of drugs that are efficient against M. abscessus remains limited. In this context, 19 oxadiazolone (OX) derivatives have been investigated for their antibacterial activity against both the rough (R) and smooth (S) variants of M. abscessus. Several OXs impair extracellular M. abscessus growth with moderated minimal inhibitory concentrations (MIC), or act intracellularly by inhibiting M. abscessus growth inside infected macrophages with MIC values similar to those of imipenem. Such promising results prompted us to identify the potential target enzymes of the sole extra and intracellular inhibitor of M. abscessus growth, i.e., compound iBpPPOX, via activity-based protein profiling combined with mass spectrometry. This approach led to the identification of 21 potential protein candidates being mostly involved in M. abscessus lipid metabolism and/or in cell wall biosynthesis. Among them, the Ag85C protein has been confirmed as a vulnerable target of iBpPPOX. This study clearly emphasizes the potential of the OX derivatives to inhibit the extracellular and/or intracellular growth of M. abscessus by targeting various enzymes potentially involved in many physiological processes of this most drug-resistant mycobacterial species.
Collapse
Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
| | - Ivy Mallick
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
- IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Alexandre Guy
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Céline Crauste
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Thierry Durand
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Patrick Fourquet
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Stéphane Canaan
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
| | - Jean François Cavalier
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
- * E-mail:
| |
Collapse
|
17
|
Kwofie SK, Adobor C, Quansah E, Bentil J, Ampadu M, Miller WA, Wilson MD. Molecular docking and dynamics simulations studies of OmpATb identifies four potential novel natural product-derived anti-Mycobacterium tuberculosis compounds. Comput Biol Med 2020; 122:103811. [PMID: 32479349 DOI: 10.1016/j.compbiomed.2020.103811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 11/18/2022]
Abstract
The outer membrane protein A (OmpATb) of Mycobacterium tuberculosis is a virulence factor that neutralizes the host pH to impede the uptake of hydrophilic antitubercular drugs. Identifying natural compounds with the potential to inhibit OmpATb could allow circumvention of the porin-like activities of OmpATb. Four potential leads comprising ZINC000003958185, ZINC000000157405, ZINC000000001392 and ZINC000034268676 were obtained by virtual screening of 6394 diverse natural products. Characterization of the binding interactions of the potential leads with OmpATb revealed nine critical residues comprising ARG86, LEU110, LEU113, LEU114, ALA115, PHE142, SER145, VAL146, and PHE151. Molecular dynamics simulations also revealed very stable protein-lead complexes. Most residues contributed lower binding energies to the overall molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energies of the interactions between the molecules and OmpATb protein. Induced Fit Docking (IFD) of the compounds regenerated poses of the molecular docking using AutoDock Vina. These molecules could be starting templates for designing inhibitors to bypass the pore mediating activities of OmpATb. Based on structural similarity, ZINC000034268676 was suggested as a potential scaffold for designing efflux pump inhibitors of the gate mediating activities of OmpATb and may enhance the uptake of hydrophilic drugs to reduce the duration time of tuberculosis treatment. Furthermore, structurally similar compounds available in the DrugBank database with a similarity threshold of 0.7 have been reported to exhibit antitubercular and anti-mycobacterial activities. These biomolecules can be further characterized experimentally to corroborate their antitubercular activity. Also, the skeletons of the molecules can be adopted as sub-structures for the design of future anti-mycobacterial drugs.
Collapse
Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Physics and Engineering Science, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Courage Adobor
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Erasmus Quansah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Joana Bentil
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Michael Ampadu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Whelton A Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA
| |
Collapse
|
18
|
Alves JA, Abrão F, da Silva Moraes T, Damasceno JL, dos Santos Moraes MF, Sola Veneziani RC, Ambrósio SR, Bastos JK, Dantas Miranda ML, Gomes Martins CH. Investigation of Copaifera genus as a new source of antimycobaterial agents. Future Sci OA 2020; 6:FSO587. [PMID: 32802394 PMCID: PMC7421775 DOI: 10.2144/fsoa-2020-0018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/29/2020] [Indexed: 12/11/2022] Open
Abstract
AIM This paper reports on the antimycobacterial activity of the oleoresins and extracts obtained from Copaifera spp. MATERIALS & METHODS The minimum inhibitory concentration (MIC) and fractional inhibitory concentration index techniques helped to evaluate the effect of these oleoresins and extracts against six strains of mycobacteria that cause tuberculosis. RESULTS & CONCLUSION Among the assayed oleoresins and plant extracts, the Copaifera langsdorffii, Copaifera duckei, Copaifera reticulata and Copaifera trapezifolia oleoresins provided the lowest MIC values against some of the tested strains. The combination of Copaifera spp. samples with isoniazid did not evidence any synergistic action. Some Copaifera spp. oleoresins may represent a future source for the discovery of new antimycobacterial drugs due to their low MIC values.
Collapse
Affiliation(s)
| | - Fariza Abrão
- Research Laboratory of Applied Microbiology, University of Franca, Franca, SP, Brazil
| | - Thaís da Silva Moraes
- Research Laboratory of Applied Microbiology, University of Franca, Franca, SP, Brazil
| | | | | | | | | | - Jairo Kenupp Bastos
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Carlos Henrique Gomes Martins
- Research Laboratory of Applied Microbiology, University of Franca, Franca, SP, Brazil
- Laboratory of Research on Antimicrobial Trials (LaPEA), Institute of Biomedical Sciences – ICBIM, Federal University of Uberlândia, Uberlândia, MG, Brazil
| |
Collapse
|
19
|
Khan F, Yu H, Kim YM. Bactericidal Activity of Usnic Acid-Chitosan Nanoparticles against Persister Cells of Biofilm-Forming Pathogenic Bacteria. Mar Drugs 2020; 18:E270. [PMID: 32443816 PMCID: PMC7281555 DOI: 10.3390/md18050270] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/11/2022] Open
Abstract
The present study aimed to prepare usnic acid (UA)-loaded chitosan (CS) nanoparticles (UA-CS NPs) and evaluate its antibacterial activity against biofilm-forming pathogenic bacteria. UA-CS NPs were prepared through simple ionic gelification of UA with CS, and further characterized using Fourier transform infrared spectroscopy, X-ray diffraction, and field-emission transmission electron microscopy. The UA-CS NPs presented a loading capacity (LC) of 5.2%, encapsulation efficiency (EE) of 24%, and a spherical shape and rough surface. The maximum release of UA was higher in pH 1.2 buffer solution as compared to that in pH 6.8 and 7.4 buffer solution. The average size and zeta potential of the UA-CS NPs was 311.5 ± 49.9 nm in diameter and +27.3 ± 0.8 mV, respectively. The newly prepared UA-CS NPs exhibited antibacterial activity against persister cells obtained from the stationary phase in batch culture, mature biofilms, and antibiotic-induced gram-positive and gram-negative pathogenic bacteria. Exposure of sub-inhibitory concentrations of UA-CS NPs to the bacterial cells resulted in a change in morphology. The present study suggests an alternative method for the application of UA into nanoparticles. Furthermore, the anti-persister activity of UA-CS NPs may be another possible strategy for the treatment of infections caused by biofilm-forming pathogenic bacteria.
Collapse
Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan 48513, Korea;
| | - Hongsik Yu
- Food Safety and Processing Research Division, National Institute of Fisheries Science, Busan 46083, Korea;
| | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan 48513, Korea;
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Korea
| |
Collapse
|
20
|
Plakinamine P, A Steroidal Alkaloid with Bactericidal Activity against Mycobacterium tuberculosis. Mar Drugs 2019; 17:md17120707. [PMID: 31888140 PMCID: PMC6950683 DOI: 10.3390/md17120707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 12/04/2022] Open
Abstract
Tuberculosis is the leading cause of death due to infectious disease worldwide. There is an urgent need for more effective compounds against this pathogen to control the disease. Investigation of the anti-mycobacterial activity of a deep-water sponge of the genus Plakina revealed the presence of a new steroidal alkaloid of the plakinamine class, which we have given the common name plakinamine P. Its structure is most similar to plakinamine L, which also has an acyclic side chain. Careful dissection of the nuclear magnetic resonance data, collected in multiple solvents, suggests that the dimethyl amino group at the 3 position is in an equatorial rather than axial position unlike previously reported plakinamines. Plakinamine P was bactericidal against M. tuberculosis, and exhibited moderate activity against other mycobacterial pathogens, such as M. abscessus and M. avium. Furthermore, it had low toxicity against J774 macrophages, yielding a selectivity index (SI, or IC50/MIC) of 8.4. In conclusion, this work provides a promising scaffold to the tuberculosis drug discovery pipeline. Future work to determine the molecular target of this compound may reveal a pathway essential for M. tuberculosis survival during infection.
Collapse
|
21
|
Felix CR, Siedler BS, Barbosa LN, Timm GR, McFadden J, McBride AJA. An overview of human leptospirosis vaccine design and future perspectives. Expert Opin Drug Discov 2019; 15:179-188. [PMID: 31777290 DOI: 10.1080/17460441.2020.1694508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Introduction: It's been 20 years since the first report of a recombinant vaccine that protected against leptospirosis. Since then, numerous recombinant vaccines have been evaluated; however, no recombinant vaccine candidate has advanced to clinical trials. With the ever-increasing burden of leptospirosis, there is an urgent need for a universal vaccine against leptospirosis.Areas covered: This review covers the most promising vaccine candidates that induced significant, reproducible, protection and how advances in the field of bioinformatics has led to the discovery of hundreds of novel protein targets. The authors also discuss the most recent findings regarding the innate immune response and host-pathogen interactions and their impact on the discovery of novel vaccine candidates. In addition, the authors have identified what they believe are the most challenging problems for the discovery and development of a universal vaccine and their potential solutions.Expert opinion: A universal vaccine for leptospirosis will likely only be achieved using a recombinant vaccine as the bacterins are of limited use due to the lack of a cross-protective immune response. Although there are hundreds of novel targets, due to the lack of immune correlates and the need for more research into the basic microbiology of Leptospira spp., a universal vaccine is 10-15 years away.
Collapse
Affiliation(s)
- Carolina R Felix
- Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Pelotas, Brazil
| | - Bianca S Siedler
- Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Pelotas, Brazil.,School of Biosciences and Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Liana N Barbosa
- Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Pelotas, Brazil
| | - Gabriana R Timm
- Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Pelotas, Brazil
| | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
| | - Alan J A McBride
- Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Pelotas, Brazil
| |
Collapse
|
22
|
Khan MT, Kaushik AC, Bhatti AI, Zhang YJ, Zhang S, Wei AJ, Malik SI, Wei DQ. Marine Natural Products and Drug Resistance in Latent Tuberculosis. Mar Drugs 2019; 17:md17100549. [PMID: 31561525 PMCID: PMC6836121 DOI: 10.3390/md17100549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022] Open
Abstract
Pyrazinamide (PZA) is the only drug for the elimination of latent Mycobacterium tuberculosis (MTB) isolates. However, due to the increased number of PZA-resistance, the chances of the success of global TB elimination seems to be more prolonged. Recently, marine natural products (MNPs) as an anti-TB agent have received much attention, where some compounds extracted from marine sponge, Haliclona sp. exhibited strong activity under aerobic and hypoxic conditions. In this study, we screened articles from 1994 to 2019 related to marine natural products (MNPs) active against latent MTB isolates. The literature was also mined for the major regulators to map them in the form of a pathway under the dormant stage. Five compounds were found to be more suitable that may be applied as an alternative to PZA for the better management of resistance under latent stage. However, the mechanism of actions behind these compounds is largely unknown. Here, we also applied synthetic biology to analyze the major regulatory pathway under latent TB that might be used for the screening of selective inhibitors among marine natural products (MNPs). We identified key regulators of MTB under latent TB through extensive literature mining and mapped them in the form of regulatory pathway, where SigH is negatively regulated by RshA. PknB, RshA, SigH, and RNA polymerase (RNA-pol) are the major regulators involved in MTB survival under latent stage. Further studies are needed to screen MNPs active against the main regulators of dormant MTB isolates. To reduce the PZA resistance burden, understanding the regulatory pathways may help in selective targets of MNPs from marine natural sources.
Collapse
Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan; (M.T.K.); (S.I.M.)
| | - Aman Chandra Kaushik
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Aamer Iqbal Bhatti
- Department of Electrical Engineering, Capital University of Science and Technology, Islamabad 44000, Pakistan;
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China;
| | - Shulin Zhang
- Department of Immunology and Microbiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (S.Z.)
| | - Amie Jinghua Wei
- Department of Immunology and Microbiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (S.Z.)
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan; (M.T.K.); (S.I.M.)
| | - Dong Qing Wei
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Correspondence: ; Tel.: +86-21-3420-4573
| |
Collapse
|
23
|
Madani A, Ridenour JN, Martin BP, Paudel RR, Abdul Basir A, Le Moigne V, Herrmann JL, Audebert S, Camoin L, Kremer L, Spilling CD, Canaan S, Cavalier JF. Cyclipostins and Cyclophostin Analogues as Multitarget Inhibitors That Impair Growth of Mycobacterium abscessus. ACS Infect Dis 2019; 5:1597-1608. [PMID: 31299146 DOI: 10.1021/acsinfecdis.9b00172] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Twelve new Cyclophostin and Cyclipostins analogues (CyC19-30) were synthesized, thus extending our series to 38 CyCs. Their antibacterial activities were evaluated against four pathogenic mycobacteria (Mycobacterium abscessus, Mycobacterium marinum, Mycobacterium bovis BCG, and Mycobacterium tuberculosis) and two Gram negative bacteria. The CyCs displayed very low toxicity toward host cells and were only active against mycobacteria. Importantly, several CyCs were active against extracellular M. abscessus (CyC17/CyC18β/CyC25/CyC26) or intramacrophage residing mycobacteria (CyC7(α,β)/CyC8(α,β)) with minimal inhibitory concentrations (MIC50) values comparable to or better than those of amikacin or imipenem, respectively. An activity-based protein profiling combined with mass spectrometry allowed identification of the potential target enzymes of CyC17/CyC26, mostly being involved in lipid metabolism and/or in cell wall biosynthesis. Overall, these results strengthen the selective activity of the CyCs against mycobacteria, including the most drug-resistant M. abscessus, through the cumulative inhibition of a large number of Ser- and Cys-enzymes participating in key physiological processes.
Collapse
Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jeremy N. Ridenour
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Benjamin P. Martin
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Rishi R. Paudel
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Anosha Abdul Basir
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Vincent Le Moigne
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
| | - Jean-Louis Herrmann
- APHP, GHU PIFO, Hôpital Raymond-Poincaré−Hôpital Ambroise-Paré, 92100 Boulogne-Billancourt, France
- 2I, UVSQ, INSERM UMR 1173, Université Paris-Saclay, 78035 Versailles, France
| | - Stéphane Audebert
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Luc Camoin
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, 13273 Marseille Cedex 09, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS, UMR 9004, Université de Montpellier, 34293 Montpellier, France
- IRIM, INSERM, 34293 Montpellier, France
| | - Christopher D. Spilling
- Department of Chemistry and Biochemistry, University of Missouri−St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| | - Jean-François Cavalier
- Aix-Marseille Université, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France 13402 Cedex 20
| |
Collapse
|
24
|
Santucci P, Dedaki C, Athanasoulis A, Gallorini L, Munoz A, Canaan S, Cavalier J, Magrioti V. Synthesis of Long‐Chain β‐Lactones and Their Antibacterial Activities against Pathogenic Mycobacteria. ChemMedChem 2019; 14:349-358. [DOI: 10.1002/cmdc.201800720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Pierre Santucci
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Christina Dedaki
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
| | - Alexandros Athanasoulis
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
| | - Laura Gallorini
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Anaïs Munoz
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Stéphane Canaan
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | | | - Victoria Magrioti
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
| |
Collapse
|
25
|
Exploitation of Mangrove Endophytic Fungi for Infectious Disease Drug Discovery. Mar Drugs 2018; 16:md16100376. [PMID: 30308948 PMCID: PMC6212984 DOI: 10.3390/md16100376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/14/2023] Open
Abstract
There is an acute need for new and effective agents to treat infectious diseases. We conducted a screening program to assess the potential of mangrove-derived endophytic fungi as a source of new antibiotics. Fungi cultured in the presence and absence of small molecule epigenetic modulators were screened against Mycobacterium tuberculosis and the ESKAPE panel of bacterial pathogens, as well as two eukaryotic infective agents, Leishmania donovani and Naegleria fowleri. By comparison of bioactivity data among treatments and targets, trends became evident, such as the result that more than 60% of active extracts were revealed to be selective to a single target. Validating the technique of using small molecules to dysregulate secondary metabolite production pathways, nearly half (44%) of those fungi producing active extracts only did so following histone deacetylase inhibitory (HDACi) or DNA methyltransferase inhibitory (DNMTi) treatment.
Collapse
|
26
|
Lane T, Russo DP, Zorn KM, Clark AM, Korotcov A, Tkachenko V, Reynolds RC, Perryman AL, Freundlich JS, Ekins AS. Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. Mol Pharm 2018; 15:4346-4360. [PMID: 29672063 PMCID: PMC6167198 DOI: 10.1021/acs.molpharmaceut.8b00083] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tuberculosis is a global health dilemma. In 2016, the WHO reported 10.4 million incidences and 1.7 million deaths. The need to develop new treatments for those infected with Mycobacterium tuberculosis ( Mtb) has led to many large-scale phenotypic screens and many thousands of new active compounds identified in vitro. However, with limited funding, efforts to discover new active molecules against Mtb needs to be more efficient. Several computational machine learning approaches have been shown to have good enrichment and hit rates. We have curated small molecule Mtb data and developed new models with a total of 18,886 molecules with activity cutoffs of 10 μM, 1 μM, and 100 nM. These data sets were used to evaluate different machine learning methods (including deep learning) and metrics and to generate predictions for additional molecules published in 2017. One Mtb model, a combined in vitro and in vivo data Bayesian model at a 100 nM activity yielded the following metrics for 5-fold cross validation: accuracy = 0.88, precision = 0.22, recall = 0.91, specificity = 0.88, kappa = 0.31, and MCC = 0.41. We have also curated an evaluation set ( n = 153 compounds) published in 2017, and when used to test our model, it showed the comparable statistics (accuracy = 0.83, precision = 0.27, recall = 1.00, specificity = 0.81, kappa = 0.36, and MCC = 0.47). We have also compared these models with additional machine learning algorithms showing Bayesian machine learning models constructed with literature Mtb data generated by different laboratories generally were equivalent to or outperformed deep neural networks with external test sets. Finally, we have also compared our training and test sets to show they were suitably diverse and different in order to represent useful evaluation sets. Such Mtb machine learning models could help prioritize compounds for testing in vitro and in vivo.
Collapse
Affiliation(s)
- Thomas Lane
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel P. Russo
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ, 08102, USA
| | - Kimberley M. Zorn
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| | - Alex M. Clark
- Molecular Materials Informatics, Inc., 1900 St. Jacques #302, Montreal H3J 2S1, Quebec, Canada
| | - Alexandru Korotcov
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Valery Tkachenko
- Science Data Software, LLC, 14914 Bradwill Court, Rockville, MD 20850, USA
| | - Robert C. Reynolds
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, NP 2540 J, 1720 2Avenue South, Birmingham, AL 35294-3300, USA
| | - Alexander L. Perryman
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology and Neuroscience, Rutgers University-New Jersey Medical School, Newark, New Jersey 07103, USA
- Division of Infectious Diseases, Department of Medicine, and the Ruy V. Lourenço Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University–New Jersey Medical School, Newark, New Jersey 07103, USA
| | - and Sean Ekins
- Collaborations Pharmaceuticals, Inc., Main Campus Drive, Lab 3510 Raleigh, NC 27606, USA
| |
Collapse
|
27
|
Evidence for Inhibition of Topoisomerase 1A by Gold(III) Macrocycles and Chelates Targeting Mycobacterium tuberculosis and Mycobacterium abscessus. Antimicrob Agents Chemother 2018; 62:AAC.01696-17. [PMID: 29483110 DOI: 10.1128/aac.01696-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/08/2018] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium tuberculosis and the fast-growing species Mycobacterium abscessus are two important human pathogens causing persistent pulmonary infections that are difficult to cure and require long treatment times. The emergence of drug-resistant M. tuberculosis strains and the high level of intrinsic resistance of M. abscessus call for novel drug scaffolds that effectively target both pathogens. In this study, we evaluated the activity of bis(pyrrolide-imine) gold(III) macrocycles and chelates, originally designed as DNA intercalators capable of targeting human topoisomerase types I and II (Topo1 and Topo2), against M. abscessus and M. tuberculosis We identified a total of 5 noncytotoxic compounds active against both mycobacterial pathogens under replicating in vitro conditions. We chose one of these hits, compound 14, for detailed analysis due to its potent bactericidal mode of inhibition and scalable synthesis. The clinical relevance of this compound was demonstrated by its ability to inhibit a panel of diverse M. tuberculosis and M. abscessus clinical isolates. Prompted by previous data suggesting that compound 14 may target topoisomerase/gyrase enzymes, we demonstrated that it lacked cross-resistance with fluoroquinolones, which target the M. tuberculosis gyrase. In vitro enzyme assays confirmed the potent activity of compound 14 against bacterial topoisomerase 1A (Topo1) enzymes but not gyrase. Novel scaffolds like compound 14 with potent, selective bactericidal activity against M. tuberculosis and M. abscessus that act on validated but underexploited targets like Topo1 represent a promising starting point for the development of novel therapeutics for infections by pathogenic mycobacteria.
Collapse
|
28
|
MacGilvary NJ, Tan S. Fluorescent Mycobacterium tuberculosis reporters: illuminating host-pathogen interactions. Pathog Dis 2018; 76:4919729. [PMID: 29718182 PMCID: PMC6086090 DOI: 10.1093/femspd/fty017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/24/2018] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of Mycobacterium tuberculosis (Mtb) is intrinsically linked to its intimate and enduring interaction with its host, and understanding Mtb-host interactions at a molecular level is critical to attempts to decrease the significant burden of tuberculosis disease. The marked heterogeneity that exists in lesion progression and outcome during Mtb infection necessitates the development of methods that enable in situ analyses of Mtb biology and host response within the spatial context of tissue structure. Fluorescent reporter Mtb strains have thus come to the forefront as an approach with broad utility for the study of the Mtb-host interface, enabling visualization of the bacteria during infection, and contributing to the discovery of several facets such as non-uniformity in microenvironments and Mtb physiology in vivo, and their relation to the host immune response or therapeutic intervention. We review here the different types of fluorescent reporters and ways in which they have been utilized in Mtb studies, and expand on how they may further be exploited in combination with novel imaging and other methodologies to illuminate key aspects of Mtb-host interactions.
Collapse
Affiliation(s)
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| |
Collapse
|
29
|
Abstract
![]()
Current tuberculosis
(TB) drug development efforts are not sufficient
to end the global TB epidemic. Recent efforts have focused on the
development of whole-cell screening assays because biochemical, target-based
inhibitor screens during the last two decades have not delivered new
TB drugs. Mycobacterium tuberculosis (Mtb), the causative
agent of TB, encounters diverse microenvironments and can be found
in a variety of metabolic states in the human host. Due to the complexity
and heterogeneity of Mtb infection, no single model can fully recapitulate
the in vivo conditions in which Mtb is found in TB patients, and there
is no single “standard” screening condition to generate
hit compounds for TB drug development. However, current screening
assays have become more sophisticated as researchers attempt to mirror
the complexity of TB disease in the laboratory. In this review, we
describe efforts using surrogates and engineered strains of Mtb to
focus screens on specific targets. We explain model culture systems
ranging from carbon starvation to hypoxia, and combinations thereof,
designed to represent the microenvironment which Mtb encounters in
the human body. We outline ongoing efforts to model Mtb infection
in the lung granuloma. We assess these different models, their ability
to generate hit compounds, and needs for further TB drug development,
to provide direction for future TB drug discovery.
Collapse
Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
| | - Nicole S Sampson
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States.,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University , Stellenbosch 7600, South Africa
| |
Collapse
|
30
|
Gupta R, Netherton M, Byrd TF, Rohde KH. Reporter-Based Assays for High-Throughput Drug Screening against Mycobacterium abscessus. Front Microbiol 2017; 8:2204. [PMID: 29176967 PMCID: PMC5687050 DOI: 10.3389/fmicb.2017.02204] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/26/2017] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium abscessus is a non-tuberculous mycobacterium that causes pulmonary and non-pulmonary infections. M. abscessus is resistant to many chemotherapeutic agents and the current treatment options show poor clinical outcomes. Thus, there is a dire need to find new antimicrobials effective at killing M. abscessus. Screening drug libraries to identify potential antimicrobials has been impeded by the lack of validated HTS assays for M. abscessus. In this study, we developed two 384-well high-throughput screening assays using fluorescent and bioluminescent reporter strains of M. abscessus for drug discovery. Optimization of inoculum size, incubation time and the volume-per-well based on Z-factor and signal intensity yielded two complementary, robust tools for M. abscessus drug discovery with Z-factor > 0.8. The MIC of known drugs, amikacin and clarithromycin, as determined by bioluminescence was in agreement with the published MIC values. A proof-of-concept screen of 2,093 natural product-inspired compounds was conducted using the 384-well bioluminescent assay to identify novel scaffolds active against M. abscessus. Five active "hit" compounds identified in this pilot screen were confirmed and characterized by a CFU assay and MIC determination. Overall, we developed and validated a 384-well screen that offers simple, sensitive and fast screening of compounds for activity against this emerging pathogen. To our knowledge, this is the first reporter-based high-throughput screening study aimed at M. abscessus drug discovery.
Collapse
Affiliation(s)
- Rashmi Gupta
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Mandy Netherton
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| | - Thomas F Byrd
- Division of Infectious Diseases, Department of Internal Medicine, The University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, United States
| |
Collapse
|
31
|
Martínez-Poveda B, Quesada AR, Medina MÁ. Pleiotropic Role of Puupehenones in Biomedical Research. Mar Drugs 2017; 15:md15100325. [PMID: 29065486 PMCID: PMC5666431 DOI: 10.3390/md15100325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/27/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022] Open
Abstract
Marine sponges represent a vast source of metabolites with very interesting potential biomedical applications. Puupehenones are sesquiterpene quinones isolated from sponges of the orders Verongida and Dictyoceratida. This family of chemical compounds is composed of a high number of metabolites, including puupehenone, the most characteristic compound of the family. Chemical synthesis of puupehenone has been reached by different routes, and the special chemical reactivity of this molecule has allowed the synthesis of many puupehenone-derived compounds. The biological activities of puupehenones are very diverse, including antiangiogenic, antitumoral, antioxidant, antimicrobial, immunomodulatory and antiatherosclerotic effects. Despite the very important roles described for puupehenones concerning different pathologies, the exact mechanism of action of these compounds and the putative therapeutic effects in vivo remain to be elucidated. This review offers an updated and global view about the biology of puupehenones and their therapeutic possibilities in human diseases such as cancer.
Collapse
Affiliation(s)
- Beatriz Martínez-Poveda
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Andalucía Tech, and IBIMA; E-29071 Málaga, Spain.
| | - Ana R Quesada
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Andalucía Tech, and IBIMA; E-29071 Málaga, Spain.
- Unidad 741 de CIBER "de Enfermedades Raras", E-29071 Málaga, Spain.
| | - Miguel Ángel Medina
- Department of Molecular Biology and Biochemistry, Faculty of Sciences, University of Málaga, Andalucía Tech, and IBIMA; E-29071 Málaga, Spain.
- Unidad 741 de CIBER "de Enfermedades Raras", E-29071 Málaga, Spain.
| |
Collapse
|