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Cheng X, Gao P, Sun L, Tian Y, Zhan P, Liu X. Identification of spirocyclic or phosphate substituted quinolizine derivatives as novel HIV-1 integrase inhibitors: a patent evaluation of WO2016094197A1, WO2016094198A1 and WO2016154527A1. Expert Opin Ther Pat 2017; 27:1277-1286. [PMID: 28749251 DOI: 10.1080/13543776.2017.1360283] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Highly active antiretroviral therapy (HAART) has been widely adopted to control the HIV-1 infection successfully. HIV-1 integrase (IN) inhibitors are primary drugs in HAART regimens targeting integration step in the HIV-1 life cycle. However, due to the emergence of viral resistance and cross-resistance amongst drugs, there is a pressing need for new and potent IN inhibitors. This review covers the three patents describing spirocyclic and phosphate substituted quinolizine derivatives as novel HIV-1 IN inhibitors for the discovery of new anti-HIV-1 drug candidates. Areas covered: This review is focused on spirocyclic and phosphate substituted quinolizine derivatives bearing the same metal chelation scaffold as novel HIV-1 IN inhibitors. Expert opinion: Generally, privileged structure-based optimizations have emerged as an effective approach to discover newly antiviral agents. More generally, due to the similar Mg2+ catalytic active centers of endoribonucleases, some divalent metal ion chelators were found to be versatile binders targeting multiple metalloenzymes. Therefore, privileged structure-based scaffold re-evolution is an important tactic to identify new chemotypes, to explore unknown biological activities, or to provide effective ligands for multiple targets by modifying the existing active compounds.
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Affiliation(s)
- Xiqiang Cheng
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ping Gao
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Ye Tian
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , Shandong , P. R. China
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52
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Anti-tubercular drug discovery: in silico implications and challenges. Eur J Pharm Sci 2017; 104:1-15. [PMID: 28341614 DOI: 10.1016/j.ejps.2017.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them. To overcome this drug-resistance, efforts are continuously being made to develop new therapeutics. New drug-targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target-based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed.
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53
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Glyoxylate detoxification is an essential function of malate synthase required for carbon assimilation in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2017; 114:E2225-E2232. [PMID: 28265055 DOI: 10.1073/pnas.1617655114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The glyoxylate shunt is a metabolic pathway of bacteria, fungi, and plants used to assimilate even-chain fatty acids (FAs) and has been implicated in persistence of Mycobacterium tuberculosis (Mtb). Recent work, however, showed that the first enzyme of the glyoxylate shunt, isocitrate lyase (ICL), may mediate survival of Mtb during the acute and chronic phases of infection in mice through physiologic functions apart from fatty acid metabolism. Here, we report that malate synthase (MS), the second enzyme of the glyoxylate shunt, is essential for in vitro growth and survival of Mtb on even-chain fatty acids, in part, for a previously unrecognized activity: mitigating the toxicity of glyoxylate excess arising from metabolism of even-chain fatty acids. Metabolomic profiling revealed that MS-deficient Mtb cultured on fatty acids accumulated high levels of the ICL aldehyde endproduct, glyoxylate, and increased levels of acetyl phosphate, acetoacetyl coenzyme A (acetoacetyl-CoA), butyryl CoA, acetoacetate, and β-hydroxybutyrate. These changes were indicative of a glyoxylate-induced state of oxaloacetate deficiency, acetate overload, and ketoacidosis. Reduction of intrabacterial glyoxylate levels using a chemical inhibitor of ICL restored growth of MS-deficient Mtb, despite inhibiting entry of carbon into the glyoxylate shunt. In vivo depletion of MS resulted in sterilization of Mtb in both the acute and chronic phases of mouse infection. This work thus identifies glyoxylate detoxification as an essential physiologic function of Mtb malate synthase and advances its validation as a target for drug development.
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54
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Ju H, Zhang J, Huang B, Kang D, Huang B, Liu X, Zhan P. Inhibitors of Influenza Virus Polymerase Acidic (PA) Endonuclease: Contemporary Developments and Perspectives. J Med Chem 2017; 60:3533-3551. [PMID: 28118010 DOI: 10.1021/acs.jmedchem.6b01227] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Influenza virus (IFV) causes periodic global influenza pandemics, resulting in substantial socioeconomic loss and burden on medical facilities. Yearly variation in the effectiveness of vaccines, slow responsiveness to vaccination in cases of pandemic IFV, and emerging resistance to available drugs highlight the need to develop additional small-molecular inhibitors that act on IFV proteins. One promising target is polymerase acidic (PA) endonuclease, which is a bridged dinuclear metalloenzyme that plays a crucial role in initiating IFV replication. During the past decade, intensive efforts have been made to develop small-molecular inhibitors of this endonuclease as candidate agents for treatment of IFV infection. Here, we review the current status of development of PA endonuclease inhibitors and we discuss the applicability of newer medicinal-chemistry strategies for the discovery more potent, selective, and safer inhibitors.
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Affiliation(s)
- Han Ju
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Bing Huang
- Poultry Institute, Shandong Academy of Agricultural Sciences , 1, Jiaoxiao Road, 250023, Jinan, Shandong, P. R. China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University , 44, West Culture Road, 250012, Jinan, Shandong, P. R. China
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55
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Evans JC, Trujillo C, Wang Z, Eoh H, Ehrt S, Schnappinger D, Boshoff HIM, Rhee KY, Barry CE, Mizrahi V. Validation of CoaBC as a Bactericidal Target in the Coenzyme A Pathway of Mycobacterium tuberculosis. ACS Infect Dis 2016; 2:958-968. [PMID: 27676316 PMCID: PMC5153693 DOI: 10.1021/acsinfecdis.6b00150] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Mycobacterium tuberculosis relies on its own ability to biosynthesize coenzyme A to meet the
needs of the myriad enzymatic reactions that depend on this cofactor
for activity. As such, the essential pantothenate and coenzyme A biosynthesis
pathways have attracted attention as targets for tuberculosis drug
development. To identify the optimal step for coenzyme A pathway disruption
in M. tuberculosis, we constructed
and characterized a panel of conditional knockdown mutants in coenzyme
A pathway genes. Here, we report that silencing of coaBC was bactericidal in vitro, whereas silencing of panB, panC, or coaE was bacteriostatic
over the same time course. Silencing of coaBC was
likewise bactericidal in vivo, whether initiated at infection or during
either the acute or chronic stages of infection, confirming that CoaBC
is required for M. tuberculosis to grow and persist in mice and arguing against significant CoaBC
bypass via transport and assimilation of host-derived pantetheine
in this animal model. These results provide convincing genetic validation
of CoaBC as a new bactericidal drug target.
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Affiliation(s)
- Joanna C. Evans
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Carolina Trujillo
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Zhe Wang
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Hyungjin Eoh
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Sabine Ehrt
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
| | - Helena I. M. Boshoff
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kyu Y. Rhee
- Department of Microbiology
and Immunology, Weill Cornell Medical College, New York, New York 10065, United States
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, New York 10065, United States
| | - Clifton E. Barry
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
- Tuberculosis
Research Section, Laboratory of Clinical Infectious Diseases, National
Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
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56
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Recent advancements in the development of anti-tuberculosis drugs. Bioorg Med Chem Lett 2016; 27:370-386. [PMID: 28017531 DOI: 10.1016/j.bmcl.2016.11.084] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Modern chemotherapy has significantly improved patient outcomes against drug-sensitive tuberculosis. However, the rapid emergence of drug-resistant tuberculosis, together with the bacterium's ability to persist and remain latent present a major public health challenge. To overcome this problem, research into novel anti-tuberculosis targets and drug candidates is thus of paramount importance. This review article provides an overview of tuberculosis highlighting the recent advances and tools that are employed in the field of anti-tuberculosis drug discovery. The predominant focus is on anti-tuberculosis agents that are currently in the pipeline, i.e. clinical trials.
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57
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Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry 2016; 55:6056-6069. [PMID: 27753291 DOI: 10.1021/acs.biochem.6b00624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.
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Affiliation(s)
- Karan Kapoor
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
| | - Michael R Duff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Amit Upadhyay
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States
| | - Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Arnold M Saxton
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Elizabeth E Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
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58
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Huang HL, Krieger IV, Parai MK, Gawandi VB, Sacchettini JC. Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange. J Biol Chem 2016; 291:27421-27432. [PMID: 27738104 PMCID: PMC5207166 DOI: 10.1074/jbc.m116.750877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/28/2016] [Indexed: 11/06/2022] Open
Abstract
Fragment screening and high throughput screening are complementary approaches that combine with structural biology to explore the binding capabilities of an active site. We have used a fragment-based approach on malate synthase (GlcB) from Mycobacterium tuberculosis and discovered several novel binding chemotypes. In addition, the crystal structures of GlcB in complex with these fragments indicated conformational changes in the active site that represent the enzyme conformations during catalysis. Additional structures of the complex with malate and of the apo form of GlcB supported that hypothesis. Comparative analysis of GlcB structures in complex with 18 fragments allowed us to characterize the preferred chemotypes and their binding modes. The fragment structures showed a hydrogen bond to the backbone carbonyl of Met-631. We successfully incorporated an indole group from a fragment into an existing phenyl-diketo acid series. The resulting indole-containing inhibitor was 100-fold more potent than the parent phenyl-diketo acid with an IC50 value of 20 nm.
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Affiliation(s)
| | - Inna V Krieger
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - Maloy K Parai
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - Vijay B Gawandi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
| | - James C Sacchettini
- From the Departments of Chemistry and .,Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77845
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59
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Islam MM, Hameed HMA, Mugweru J, Chhotaray C, Wang C, Tan Y, Liu J, Li X, Tan S, Ojima I, Yew WW, Nuermberger E, Lamichhane G, Zhang T. Drug resistance mechanisms and novel drug targets for tuberculosis therapy. J Genet Genomics 2016; 44:21-37. [PMID: 28117224 DOI: 10.1016/j.jgg.2016.10.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/26/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
Drug-resistant tuberculosis (TB) poses a significant challenge to the successful treatment and control of TB worldwide. Resistance to anti-TB drugs has existed since the beginning of the chemotherapy era. New insights into the resistant mechanisms of anti-TB drugs have been provided. Better understanding of drug resistance mechanisms helps in the development of new tools for the rapid diagnosis of drug-resistant TB. There is also a pressing need in the development of new drugs with novel targets to improve the current treatment of TB and to prevent the emergence of drug resistance in Mycobacterium tuberculosis. This review summarizes the anti-TB drug resistance mechanisms, furnishes some possible novel drug targets in the development of new agents for TB therapy and discusses the usefulness using known targets to develop new anti-TB drugs. Whole genome sequencing is currently an advanced technology to uncover drug resistance mechanisms in M. tuberculosis. However, further research is required to unravel the significance of some newly discovered gene mutations in their contribution to drug resistance.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, The Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, Stony Brook University-State University of New York, Stony Brook, NY 11794-3400, USA
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Eric Nuermberger
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD 21231-1002, USA
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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60
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Therapeutic Potential of the Mycobacterium tuberculosis Mycolic Acid Transporter, MmpL3. Antimicrob Agents Chemother 2016; 60:5198-207. [PMID: 27297488 DOI: 10.1128/aac.00826-16] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/08/2016] [Indexed: 11/20/2022] Open
Abstract
In recent years, whole-cell-based screens for novel small molecule inhibitors active against Mycobacterium tuberculosis in culture followed by the whole-genome sequencing of spontaneous resistant mutants have identified multiple chemical scaffolds thought to kill the bacterium through the inactivation of the mycolic acid transporter, MmpL3. Consistent with the fact that MmpL3 is required for the formation of the mycobacterial outer membrane, we have conclusively shown in this study, using conditionally regulated knockdown mutants, that mmpL3 is required for the replication and viability of M. tuberculosis, both under standard laboratory growth conditions and during the acute and chronic phases of infection in mice. Speaking for the vulnerability of this target, silencing mmpL3 had a rapid bactericidal effect on actively replicating cells in vitro and reduced by 3 to 5 logs in less than 4 weeks the bacterial loads of acutely and chronically infected mouse lungs, respectively. Depletion of MmpL3 further rendered M. tuberculosis hypersusceptible to MmpL3 inhibitors. The exquisite vulnerability of MmpL3 at all stages of the infection establishes this transporter as an attractive new target with the potential to improve and shorten current drug-susceptible and drug-resistant tuberculosis chemotherapies.
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61
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Lv C, Wang P, Wang W, Su R, Ge Y, Zhu Y, Zhu G. Two isocitrate dehydrogenases from a plant pathogen Xanthomonas campestris pv. campestris 8004. Bioinformatic analysis, enzymatic characterization, and implication in virulence. J Basic Microbiol 2016; 56:975-85. [PMID: 27282849 DOI: 10.1002/jobm.201500648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/28/2016] [Indexed: 12/16/2022]
Abstract
Isocitrate dehydrogenase (IDH) is a key enzyme in the tricarboxylate (TCA) cycle, which may play an important role in the virulence of pathogenic bacteria. Here, two structurally different IDHs from a plant pathogen Xanthomonas campestris pv. campestris 8004 (XccIDH1 and XccIDH2) were characterized in detail. The recombinant XccIDH1 forms homodimer in solution, while the recombinant XccIDH2 is a typical monomer. Phylogenetic analysis showed that XccIDH1 belongs to the type I IDH subfamily and XccIDH2 groups into the monomeric IDH clade. Kinetic characterization demonstrated that XccIDH1's specificity towards NAD(+) was 110-fold greater than NADP(+) , while XccIDH2's specificity towards NADP(+) was 353-fold greater than NAD(+) . The putative coenzyme discriminating amino acids (Asp268, Ile269 and Ala275 for XccIDH1, and Lys589, His590 and Arg601 for XccIDH2) were studied by site-directed mutagenesis. The coenzyme specificities of the two mutants, mXccIDH1 and mXccIDH2, were completely reversed from NAD(+) to NADP(+) , and NADP(+) to NAD(+) , respectively. Furthermore, Ser80 of XccIDH1, and Lys256 and Tyr421 of XccIDH2, were the determinants for the substrate binding. The detailed biochemical properties, such as optimal pH and temperature, thermostability, and metal ion effects, of XccIDH1 and XccIDH2 were further investigated. The possibility of taking the two IDHs into consideration as the targets for drug development to control the plant diseases caused by Xcc 8004 were described and discussed thoroughly.
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Affiliation(s)
- Changqi Lv
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China
| | - Peng Wang
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China
| | - Wencai Wang
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China
| | - Ruirui Su
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China
| | - Yadong Ge
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China
| | - Youming Zhu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Stomatological Hospital, Anhui Medical University, China.
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, College of Life Sciences, Anhui Normal University, China.
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62
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Anion–π interactions in complexes of proteins and halogen-containing amino acids. J Biol Inorg Chem 2016; 21:357-68. [DOI: 10.1007/s00775-016-1346-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
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63
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Abstract
Genetic strategies have yet to come into their own as tools for antibiotic development. While holding a lot of initial promise, they have only recently started to bear fruit in the quest for new drug targets. An ever-increasing body of knowledge is showing that genetics can lead to significant improvements in the success and efficiency of drug discovery. Techniques such as high-frequency transposon mutagenesis and expression modulation have matured and have been applied successfully not only to the identification and characterization of new targets, but also to their validation as tractable weaknesses of bacteria. Past experience shows that choosing targets must not rely on gene essentiality alone, but rather needs to incorporate knowledge of the system as a whole. The ability to manipulate genes and their expression is key to ensuring that we understand the entire set of processes that are affected by drug treatment. Focusing on exacerbating these perturbations, together with the identification of new targets to which resistance has not yet occurred--both enabled by genetic approaches--may point us toward the successful development of new combination therapies engineered based on underlying biology.
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64
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Giese M, Albrecht M, Rissanen K. Experimental investigation of anion–π interactions – applications and biochemical relevance. Chem Commun (Camb) 2016; 52:1778-95. [DOI: 10.1039/c5cc09072e] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Anion–π interactions, intuitively repulsive forces, turned from controversial to a well-established non-covalent interaction over the past quarter of a century.
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Affiliation(s)
- M. Giese
- Institut für Organische Chemie
- Universität Duisburg Essen
- 45141 Essen
- Germany
| | - M. Albrecht
- Institut für Organische Chemie
- RWTH Aachen University
- 52074 Aachen
- Germany
| | - K. Rissanen
- University of Jyvaskyla
- Department of Chemistry
- Nanoscience Center
- P.O. Box. 35
- FI-40014 University of Jyvaskyla
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65
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Singh KS, Singh SK. The Mycobacterium tuberculosis H37Ra gene MRA_1916 causes growth defects upon down-regulation. Sci Rep 2015; 5:16131. [PMID: 26531045 PMCID: PMC4632087 DOI: 10.1038/srep16131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 10/08/2015] [Indexed: 11/09/2022] Open
Abstract
D-amino acid oxidases play an important role in converting D-amino acids to their corresponding α-keto acids. MRA_1916 of Mycobacterium tuberculosis H37Ra (Mtb-Ra) is annotated to be a D-amino acid oxidase (DAO). However, not much information is available about its physiological role during Mtb-Ra growth and survival. The present study was taken-up to understand the role of DAO during different stages of growth and effect of its down-regulation on growth. Recombinant Mtb-Ra strains with DAO and GlcB (malate synthase: MRA_1848) gene knockdown were developed and their growth was studied using Microtiter Alamar Blue Assay (MABA) with glycerol, acetate and glycine as a carbon source. Ethyl bromopyruvate (BrP) was used as an inhibitor of GlcB. MABA study showed inhibition of wild-type (WT) and knockdowns in the presence of BrP (2.5mM). However, growth inhibition of WT was less noticeable at lower concentrations of BrP. Mtb-Ra with DAO knockdown showed poor utilization of glycine in the presence of BrP. The DAO localization study showed its prominent distribution in cytosolic fraction and to some extent in cell wall and membrane fractions. Growth profile of WT under oxygen and nutritional stress showed changes in expression of DAO, GlcB, PckA (phosphoenolpyruvate carboxykinase: MRA_0219) and GlyA1 (serine hydroxymethyltransferase: MRA_1104).
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Affiliation(s)
- Kumar Sachin Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, U.P., India, Pin: 226031
| | - Sudheer Kumar Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, U.P., India, Pin: 226031
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66
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Evans JC, Mizrahi V. The application of tetracyclineregulated gene expression systems in the validation of novel drug targets in Mycobacterium tuberculosis. Front Microbiol 2015; 6:812. [PMID: 26300875 PMCID: PMC4523840 DOI: 10.3389/fmicb.2015.00812] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022] Open
Abstract
Although efforts to identify novel therapies for the treatment of tuberculosis have led to the identification of several promising drug candidates, the identification of high-quality hits from conventional whole-cell screens remains disappointingly low. The elucidation of the genome sequence of Mycobacterium tuberculosis (Mtb) facilitated a shift to target-based approaches to drug design but these efforts have proven largely unsuccessful. More recently, regulated gene expression systems that enable dose-dependent modulation of gene expression have been applied in target validation to evaluate the requirement of individual genes for the growth of Mtb both in vitro and in vivo. Notably, these systems can also provide a measure of the extent to which putative targets must be depleted in order to manifest a growth inhibitory phenotype. Additionally, the successful implementation of Mtb strains engineered to under-express specific molecular targets in whole-cell screens has enabled the simultaneous identification of cell-permeant inhibitors with defined mechanisms of action. Here, we review the application of tetracycline-regulated gene expression systems in the validation of novel drug targets in Mtb, highlighting both the strengths and limitations associated with this approach to target validation.
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Affiliation(s)
- Joanna C. Evans
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research UnitCape Town, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa
| | - Valerie Mizrahi
- South African Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research UnitCape Town, South Africa
- DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Division of Medical Microbiology, Faculty of Health Sciences, University of Cape TownCape Town, South Africa
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67
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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68
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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69
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Badri Z, Foroutan-Nejad C, Kozelka J, Marek R. On the non-classical contribution in lone-pair–π interaction: IQA perspective. Phys Chem Chem Phys 2015; 17:26183-90. [DOI: 10.1039/c5cp04489h] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Most and least electrostatic repulsive parts of a complex presented by red and blue isosurface repulsive potential energy density.
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Affiliation(s)
- Zahra Badri
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
| | - Cina Foroutan-Nejad
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
| | - Jiri Kozelka
- Université Paris Descartes
- UMR 8601 CNRS
- 75270 Paris
- France
- Department of Condensed Matter Physics
| | - Radek Marek
- CEITEC – Central European Institute of Technology
- Masaryk University
- Brno
- Czech Republic
- Department of Chemistry
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70
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Anion-π Interactions in Supramolecular Chemistry and Catalysis. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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71
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Safin DA, Pialat A, Leitch AA, Tumanov NA, Korobkov I, Filinchuk Y, Brusso JL, Murugesu M. Anion-induced AgIself-assemblies with electron deficient aromatic ligands: anion–π-system interactions as a driving force for templated coordination networks. Chem Commun (Camb) 2015; 51:9547-50. [DOI: 10.1039/c5cc01597a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1D, 2D and 3D AgIcoordination polymers were isolated using nitrogen based 3,6-bis(2′-pyrimidyl)-1,2,4,5-tetrazine and 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine ligands.
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Affiliation(s)
- Damir A. Safin
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada K1N 6N5
| | - Amélie Pialat
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada K1N 6N5
| | | | - Nikolay A. Tumanov
- Institute of Condensed Matter and Nanosciences
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
| | - Ilia Korobkov
- Department of Chemistry
- University of Ottawa
- Ottawa
- Canada K1N 6N5
| | - Yaroslav Filinchuk
- Institute of Condensed Matter and Nanosciences
- Université catholique de Louvain
- 1348 Louvain-la-Neuve
- Belgium
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72
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Zlatović MV, Borozan SZ, Nikolić MR, Stojanović SĐ. Anion–π interactions in protein–porphyrin complexes. RSC Adv 2015. [DOI: 10.1039/c5ra03373j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, we have analyzed the influence of anion–π interactions on the stability of high resolution protein–porphyrin complex crystal structures.
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Affiliation(s)
| | - Sunčica Z. Borozan
- Department of Chemistry
- Faculty of Veterinary Medicine
- University of Belgrade
- Belgrade
- Serbia
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73
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Breberina LM, Milčić MK, Nikolić MR, Stojanović SĐ. Contribution of anion-π interactions to the stability of Sm/LSm proteins. J Biol Inorg Chem 2014; 20:475-85. [PMID: 25502146 DOI: 10.1007/s00775-014-1227-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/29/2014] [Indexed: 12/29/2022]
Abstract
We have analyzed the influence of anion-π interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-π interactions than Asp. Phe has the highest occurrence in these interactions than the other two π residues. Among the anion-π residue pairs, Glu-Phe residue pair showed the maximum number of anion-π. We have found hot-spot residues forming anion-π interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-π interacting residues identified in the dataset were involved in the formation of multiple anion-π interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-π interaction energies are distance and orientation dependent. It was found that anion-π interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-π interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same π-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-π interaction to the stability of Sm/LSm proteins.
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74
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Dkhar HK, Gopalsamy A, Loharch S, Kaur A, Bhutani I, Saminathan K, Bhagyaraj E, Chandra V, Swaminathan K, Agrawal P, Parkesh R, Gupta P. Discovery of Mycobacterium tuberculosis α-1,4-glucan branching enzyme (GlgB) inhibitors by structure- and ligand-based virtual screening. J Biol Chem 2014; 290:76-89. [PMID: 25384979 DOI: 10.1074/jbc.m114.589200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
GlgB (α-1,4-glucan branching enzyme) is the key enzyme involved in the biosynthesis of α-glucan, which plays a significant role in the virulence and pathogenesis of Mycobacterium tuberculosis. Because α-glucans are implicated in the survival of both replicating and non-replicating bacteria, there exists an exigent need for the identification and development of novel inhibitors for targeting enzymes, such as GlgB, involved in this pathway. We have used the existing structural information of M. tuberculosis GlgB for high throughput virtual screening and molecular docking. A diverse database of 330,000 molecules was used for identifying novel and efficacious therapeutic agents for targeting GlgB. We also used three-dimensional shape as well as two-dimensional similarity matrix methods to identify diverse molecular scaffolds that inhibit M. tuberculosis GlgB activity. Virtual hits were generated after structure and ligand-based screening followed by filters based on interaction with human GlgB and in silico pharmacokinetic parameters. These hits were experimentally evaluated and resulted in the discovery of a number of structurally diverse chemical scaffolds that target M. tuberculosis GlgB. Although a number of inhibitors demonstrated in vitro enzyme inhibition, two compounds in particular showed excellent inhibition of in vivo M. tuberculosis survival and its ability to get phagocytosed. This work shows that in silico docking and three-dimensional chemical similarity could be an important therapeutic approach for developing inhibitors to specifically target the M. tuberculosis GlgB enzyme.
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Affiliation(s)
- Hedwin Kitdorlang Dkhar
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Anupriya Gopalsamy
- the Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Saurabh Loharch
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Amandeep Kaur
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Isha Bhutani
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Kanmani Saminathan
- the Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Ella Bhagyaraj
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Vemika Chandra
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | | | - Pushpa Agrawal
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Raman Parkesh
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
| | - Pawan Gupta
- From the Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India and
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75
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Govender VS, Ramsugit S, Pillay M. Mycobacterium tuberculosis adhesins: potential biomarkers as anti-tuberculosis therapeutic and diagnostic targets. Microbiology (Reading) 2014; 160:1821-1831. [DOI: 10.1099/mic.0.082206-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adhesion to host cells is a precursor to host colonization and evasion of the host immune response. Conversely, it triggers the induction of the immune response, a process vital to the host’s defence against infection. Adhesins are microbial cell surface molecules or structures that mediate the attachment of the microbe to host cells and thus the host–pathogen interaction. They also play a crucial role in bacterial aggregation and biofilm formation. In this review, we discuss the role of adhesins in the pathogenesis of the aetiological agent of tuberculosis, Mycobacterium tuberculosis. We also provide insight into the structure and characteristics of some of the characterized and putative M. tuberculosis adhesins. Finally, we examine the potential of adhesins as targets for the development of tuberculosis control strategies.
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Affiliation(s)
- Viveshree S. Govender
- Medical Microbiology and Infection Control, University of KwaZulu-Natal, Durban, South Africa
| | - Saiyur Ramsugit
- Medical Microbiology and Infection Control, University of KwaZulu-Natal, Durban, South Africa
| | - Manormoney Pillay
- Medical Microbiology and Infection Control, University of KwaZulu-Natal, Durban, South Africa
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76
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The phosphatidyl-myo-inositol mannosyltransferase PimA is essential for Mycobacterium tuberculosis growth in vitro and in vivo. J Bacteriol 2014; 196:3441-51. [PMID: 25049093 DOI: 10.1128/jb.01346-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The cell envelope of Mycobacterium tuberculosis contains glycans and lipids of peculiar structure that play prominent roles in the biology and pathogenesis of tuberculosis. Consequently, the chemical structure and biosynthesis of the cell wall have been intensively investigated in order to identify novel drug targets. Here, we validate that the function of phosphatidyl-myo-inositol mannosyltransferase PimA is vital for M. tuberculosis in vitro and in vivo. PimA initiates the biosynthesis of phosphatidyl-myo-inositol mannosides by transferring a mannosyl residue from GDP-Man to phosphatidyl-myo-inositol on the cytoplasmic side of the plasma membrane. To prove the essential nature of pimA in M. tuberculosis, we constructed a pimA conditional mutant by using the TetR-Pip off system and showed that downregulation of PimA expression causes bactericidality in batch cultures. Consistent with the biochemical reaction catalyzed by PimA, this phenotype was associated with markedly reduced levels of phosphatidyl-myo-inositol dimannosides, essential structural components of the mycobacterial cell envelope. In addition, the requirement of PimA for viability was clearly demonstrated during macrophage infection and in two different mouse models of infection, where a dramatic decrease in viable counts was observed upon silencing of the gene. Notably, depletion of PimA resulted in complete clearance of the mouse lungs during both the acute and chronic phases of infection. Altogether, the experimental data highlight the importance of the phosphatidyl-myo-inositol mannoside biosynthetic pathway for M. tuberculosis and confirm that PimA is a novel target for future drug discovery programs.
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Abstract
Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.
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78
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Bauzá A, Quiñonero D, Deyà PM, Frontera A. Long-Range Effects in Anion-π Interactions: Their Crucial Role in the Inhibition Mechanism ofMycobacterium TuberculosisMalate Synthase. Chemistry 2014; 20:6985-90. [DOI: 10.1002/chem.201304995] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 01/08/2023]
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79
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Lechartier B, Rybniker J, Zumla A, Cole ST. Tuberculosis drug discovery in the post-post-genomic era. EMBO Mol Med 2014; 6:158-68. [PMID: 24401837 PMCID: PMC3927952 DOI: 10.1002/emmm.201201772] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The expectation that genomics would result in new therapeutic interventions for infectious diseases remains unfulfilled. In the post-genomic era, the decade immediately following the availability of the genome sequence of Mycobacterium tuberculosis, tuberculosis (TB) drug discovery relied heavily on the target-based approach but this proved unsuccessful leading to a return to whole cell screening. Genomics underpinned screening by providing knowledge and many enabling technologies, most importantly whole genome resequencing to find resistance mutations and targets, and this resulted in a selection of leads and new TB drug candidates that are reviewed here. Unexpectedly, many new targets were found to be ‘promiscuous’ as they were inhibited by a variety of different compounds. In the post-post-genomics era, more advanced technologies have been implemented and these include high-content screening, screening for inhibitors of latency, the use of conditional knock-down mutants for validated targets and siRNA screens. In addition, immunomodulation and pharmacological manipulation of host functions are being explored in an attempt to widen our therapeutic options.
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Affiliation(s)
- Benoit Lechartier
- Ecole Polytechnique Fédérale de Lausanne Global Health Institute, Lausanne, Switzerland
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80
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Gamez P. The anion–π interaction: naissance and establishment of a peculiar supramolecular bond. Inorg Chem Front 2014. [DOI: 10.1039/c3qi00055a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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81
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Strittmatter L, Li Y, Nakatsuka NJ, Calvo SE, Grabarek Z, Mootha VK. CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity. Hum Mol Genet 2013; 23:2313-23. [PMID: 24334609 DOI: 10.1093/hmg/ddt624] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
CLYBL is a human mitochondrial enzyme of unknown function that is found in multiple eukaryotic taxa and conserved to bacteria. The protein is expressed in the mitochondria of all mammalian organs, with highest expression in brown fat and kidney. Approximately 5% of all humans harbor a premature stop polymorphism in CLYBL that has been associated with reduced levels of circulating vitamin B12. Using comparative genomics, we now show that CLYBL is strongly co-expressed with and co-evolved specifically with other components of the mitochondrial B12 pathway. We confirm that the premature stop polymorphism in CLYBL leads to a loss of protein expression. To elucidate the molecular function of CLYBL, we used comparative operon analysis, structural modeling and enzyme kinetics. We report that CLYBL encodes a malate/β-methylmalate synthase, converting glyoxylate and acetyl-CoA to malate, or glyoxylate and propionyl-CoA to β-methylmalate. Malate synthases are best known for their established role in the glyoxylate shunt of plants and lower organisms and are traditionally described as not occurring in humans. The broader role of a malate/β-methylmalate synthase in human physiology and its mechanistic link to vitamin B12 metabolism remain unknown.
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Affiliation(s)
- Laura Strittmatter
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
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82
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Devitt E. Sun sets on protein initiative, casting shadow over drug discovery. Nat Med 2013; 19:1352. [DOI: 10.1038/nm1113-1352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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83
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A Hidden Markov Model for identifying essential and growth-defect regions in bacterial genomes from transposon insertion sequencing data. BMC Bioinformatics 2013; 14:303. [PMID: 24103077 PMCID: PMC3854130 DOI: 10.1186/1471-2105-14-303] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/01/2013] [Indexed: 02/04/2023] Open
Abstract
Background Knowledge of which genes are essential to the survival of an organism is critical to understanding the function of genes, and for the identification of potential drug targets for antimicrobial treatment. Previous statistical methods for assessing essentiality based on sequencing of tranposon libraries have usually limited their assessment to strict 'essential’ or 'non-essential’ categories. However, this binary view of essentiality does not accurately represent the more nuanced ways the growth of an organism might be affected by the disruption of its genes. In addition, these methods often limit their analysis to open-reading frames. We propose a novel method for analyzing sequence data from transposon mutant libraries using a Hidden Markov Model (HMM), along with formulas to adapt the parameters of the model to different datasets for robustness. This approach allows for the clustering of insertion sites into distinct regions of essentiality across the entire genome in a statistically rigorous manner, while also allowing for the detection of growth-defect and growth-advantage regions. Results We evaluate the performance of a 4-state HMM on a sequence dataset of M. tuberculosis transposon mutants. We also test the HMM on several synthetic datasets representing different levels of transposon insertion density and sequence coverage. We show that the HMM produces results that are highly correlated with previous assignments of essentiality for this organism. We also show that it detects growth-defect and growth-advantage genes previously shown to impair or enhance growth when disrupted. Conclusions A 4-state HMM provides an improved way of analyzing Tn-seq data and assessing different levels of essentiality that enables not only the characterization of essential and non-essential genes, but also genes whose disruption leads to impairment (or enhancement) of growth.
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84
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Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32. Proc Natl Acad Sci U S A 2013; 110:11565-70. [PMID: 23798446 DOI: 10.1073/pnas.1302114110] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Infection with the bacterial pathogen Mycobacterium tuberculosis imposes an enormous burden on global public health. New antibiotics are urgently needed to combat the global tuberculosis pandemic; however, the development of new small molecules is hindered by a lack of validated drug targets. Here, we describe the identification of a 4,6-diaryl-5,7-dimethyl coumarin series that kills M. tuberculosis by inhibiting fatty acid degradation protein D32 (FadD32), an enzyme that is required for biosynthesis of cell-wall mycolic acids. These substituted coumarin inhibitors directly inhibit the acyl-acyl carrier protein synthetase activity of FadD32. They effectively block bacterial replication both in vitro and in animal models of tuberculosis, validating FadD32 as a target for antibiotic development that works in the same pathway as the established antibiotic isoniazid. Targeting new steps in well-validated biosynthetic pathways in antitubercular therapy is a powerful strategy that removes much of the usual uncertainty surrounding new targets and in vivo clinical efficacy, while circumventing existing resistance to established targets.
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85
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Abstract
There is an urgent need to develop new drugs for the treatment of tuberculosis, particularly against latent/persistent forms of the causative agent, Mycobacterium tuberculosis. In this issue of Chemistry & Biology, Krieger and colleagues use a structure-guided approach to develop novel inhibitors of malate synthase, a target in the glyoxylate shunt that is critical for pathogen survival in chronic infection.
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Abstract
The study of the noncovalent force between π-acidic aromatic systems and anions, referred to as the anion-π interaction, has recently emerged as a new branch of supramolecular chemistry. The anion-π contact is complementary to the cation-π interaction, a prominent noncovalent force involved in protein structure and enzyme function. Until recently, the scientific community had overlooked the anion-π interaction due to its ostensibly counterintuitive nature. Pioneering theoretical studies in 2002, however, established that anion-π interactions are energetically favorable (~20-70 kJ/mol) and prompted a flurry of reports in support of their existence. The interest in anion-π contacts was further fueled by the importance of anions in key chemical and biological processes and the involvement of π-rings in anion recognition and transport. Anion-π interactions hold great promise for the design of selective anion receptors, hosts or scaffolds, colorimetric sensors, and catalysts and may also affect biological functions. Currently, the area of anion-π research is highly topical in the scientific community and on a meteoric rise in the chemical literature. This Account highlights our leading findings in this burgeoning area. Our work has focused on comprehensive investigations of several unprecedented supramolecular systems, in which the anions and their close anion-π contacts are the driving elements of the final architectures. We surveyed several heterocyclic π-acidic aromatic systems amenable to anion-π contacts and explored the subtle interplay between ligand π-acidity, anion identity, and metal ions in mediating the ensuing self-assembled architectures. The reactions we performed between solvated first-row transition metal ions and the π-acidic ligands bptz (3,6-bis(2-pyridyl)-1,2,4,5-tetrazine) or bmtz (3,6-bis(2-pyrimidyl)-1,2,4,5-tetrazine) resulted in unprecedented metallacycles. Our investigations revealed that the identity of the encapsulated ion dictates the metallacycle nuclearity and close anion-π contacts are critical for the metallacycle stability. Our X-ray crystallographic, NMR spectroscopic, and mass spectrometric (MS) studies demonstrated that the tetrahedral ([BF4](-), [ClO4](-)) and octahedral ([SbF6](-), [AsF6](-), [PF6](-)) anions template discrete molecular squares and pentagons, respectively. The metal ions occupy the vertices, and bptz or bmtz moieties span the edges of the metallacycles. The encapsulated anions occupy the π-acidic cavities of the metallacycles and establish multiple close directional F/O···C(tetrazine) contacts with the edges. The observation of notable (19)F solid-state NMR chemical shifts reflects the short contacts of the encapsulated anions, findings that we corroborated by DFT calculations. The solution NMR data support the conclusion that bona fide metallacycle templation and interconversion between the metallacycles in solution occurs only in the presence of the appropriate anions. The NMR, MS, and CV data underscore the remarkable metallapentacycle stability despite the angle strain inherent in pentagons formed by octahedral metal ions. The low anion activation energies of encapsulation (ΔG(‡) ~ 50 kJ/mol) suggest that anion-π contacts assist the anion templation. We also studied reactions of Ag(I)X (X(-) = [PF6](-), [AsF6](-), [SbF6](-), [BF4](-)) with bptz or bppn (3,6-bis(2-pyridyl)-1,2-pyridazine) to assess the effect of the ligand π-acidity on the preferred structures. The X-ray data revealed that the higher π-acidity of the tetrazine ring in bptz leads to propeller-type products [Ag2(bptz)3](2+) exhibiting prominent short anion-π contacts. By contrast, the less π-acidic bppn preferentially favors grids [Ag4(bppn)4](4+) which exhibit maximized π-π interactions. Finally, we explored the reactions of the extended π-acidic heterocycle HAT(CN)6 (1,4,5,8,9,12-hexaazatriphenylene-hexacarbonitrile) with the Cl(-), Br(-), I(-) ions which lead to highly colored solutions/crystals. X-ray crystallographic studies of the HAT(CN)6/halide complexes revealed unprecedented multisite short peripheral charge-transfer and centroid anion-π contacts. In solution, the charge-transfer contacts were evidenced by electronic absorption, (13)C and halogen NMR, as well as MS data. The distinctly colored complex entities exhibit extraordinarily high association constants, which render them promising for anion-sensing receptor applications.
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Affiliation(s)
- Helen T. Chifotides
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842, United States
| | - Kim R. Dunbar
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, Texas 77842, United States
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DeJesus MA, Zhang YJ, Sassetti CM, Rubin EJ, Sacchettini JC, Ioerger TR. Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. ACTA ACUST UNITED AC 2013; 29:695-703. [PMID: 23361328 DOI: 10.1093/bioinformatics/btt043] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Next-generation sequencing affords an efficient analysis of transposon insertion libraries, which can be used to identify essential genes in bacteria. To analyse this high-resolution data, we present a formal Bayesian framework for estimating the posterior probability of essentiality for each gene, using the extreme-value distribution to characterize the statistical significance of the longest region lacking insertions within a gene. We describe a sampling procedure based on the Metropolis-Hastings algorithm to calculate posterior probabilities of essentiality while simultaneously integrating over unknown internal parameters. RESULTS Using a sequence dataset from a transposon library for Mycobacterium tuberculosis, we show that this Bayesian approach predicts essential genes that correspond well with genes shown to be essential in previous studies. Furthermore, we show that by using the extreme-value distribution to characterize genomic regions lacking transposon insertions, this method is capable of identifying essential domains within genes. This approach can be used for analysing transposon libraries in other organisms and augmenting essentiality predictions with statistical confidence scores.
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Affiliation(s)
- Michael A DeJesus
- Department of Computer Science, Texas A&M University, College Station, TX 77843, USA.
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