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References from A Multi‐Scale Computational Framework for Anti‐Persister Tuberculosis Drug Discovery. Local targets link to admitted publications; unresolved targets remain external evidence.
2D‐QSAR Modeling and Two‐Fold Classification of 1, 2, 4‐Triazole Derivatives for Antitubercular Potency Against the Dormant Stage of Mycobacterium tuberculosis
10.1007/s11030-021-10254-y · 2022 · External reference
Molecular Docking‐Based Interactions in QSAR Studies on Mycobacterium tuberculosis ATP Synthase Inhibitors
10.1080/1062936x.2022.2066175 · 2022 · External reference
Liquid Chromatography‐Mass Spectrometry‐Based Protocol to Measure Drug Accumulation in Mycobacterium Tuberculosis and Its Host Cell
10.1016/j.xpro.2022.101971 · 2023 · External reference
Hypochlorous Acid Has Emerged as a Potential Alternative to Conventional Antibiotics due to Its Broad‐Spectrum Antimicrobial Activity
2023 · External reference
Discovery of Caralluma‐Derived Pregnane Glycosides as Potent and Selective Cholinesterase Inhibitors: Integrated In Silico and In Vitro Evaluation
10.1039/d6ra01548d · 2026 · External reference
Combining Docking and Molecular Dynamic Simulations in Drug Design
10.1002/med.20067 · 2006 · External reference
Structure‐Based Cheminformatics and Molecular Dynamics Profiling of Potential SIRT6 Inhibitors
10.1007/s11030-025-11285-5 · 2025 · External reference
A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis
10.1126/science.1106753 · 2005 · External reference
Acquired Resistance of Mycobacterium tuberculosis to Bedaquiline
10.1371/journal.pone.0102135 · 2014 · External reference
Terminal Respiratory Oxidases: A Targetables Vulnerability of Mycobacterial Bioenergetics?
10.3389/fcimb.2020.589318 · 2020 · External reference
Machine Learning Methods as a Cost‐Effective Alternative to Physics‐Based Binding Free Energy Calculations
10.3390/molecules29040830 · 2024 · External reference
A Structure‐Based Drug Discovery Paradigm
10.3390/ijms20112783 · 2019 · External reference
In Silico Approach for Developing New Anti‐Tuberculosis Drug Candidates: 3D‐QSAR, Molecular Docking and ADME Studies of Pretomanid Derivatives
2024 · External reference
Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery
10.3390/membranes13110851 · 2023 · External reference
Supramolecular Organisation and Dynamics of Mannosylated Phosphatidylinositol Lipids in the Mycobacterial Plasma Membrane
10.1016/j.bpj.2022.11.897 · 2023 · External reference
10.7554/elife.108644.1
10.7554/elife.108644.1 · External reference
Addressing Latent Tuberculosis: New Advances in Mimicking the Disease, Discovering Key Targets, and Designing Hit Compounds
10.3390/ijms21228854 · 2020 · External reference
Harnessing Natural Product Compounds to Target Dormancy Survival Regulator (DosR) in Latent Tuberculosis Infection (LTBI): An In Silico Strategy Against Dormancy
10.3390/arm93030019 · 2025 · External reference
Integrated Virtual Screening of Anthraquinone Derivatives for Anticancer Drug Discovery
10.1142/s2737416525501261 · 2026 · External reference
Machine Learning in Computer‐Aided Synthesis Planning
10.1021/acs.accounts.8b00087 · 2018 · External reference
Spontaneous Emergence of Multiple Drug Resistance in Tuberculosis Before and During Therapy
10.1371/journal.pone.0018327 · 2011 · External reference
Mechanism of Mycobacterial ATP Synthase Inhibition by Squaramides and Second Generation Diarylquinolines
10.15252/embj.2023113687 · 2023 · External reference
Constant pH Molecular Dynamics Simulations: Current Status and Recent Applications
10.1016/j.sbi.2022.102498 · 2022 · External reference
Hypoxia Is Not a Main Stress When Mycobacterium tuberculosis Is in a Dormancy‐Like Long‐Chain Fatty Acid Environment
10.3389/fcimb.2018.00449 · 2018 · External reference
Interpretation of pH–Activity Profiles for Acid–Base Catalysis From Molecular Simulations
10.1021/bi5012833 · 2015 · External reference
Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy
10.1021/jacs.6b02682 · 2016 · External reference
Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target
10.3390/ijms23063166 · 2022 · External reference
Unresolved reference
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The MM/PBSA and MM/GBSA Methods to Estimate Ligand‐Binding Affinities
10.1517/17460441.2015.1032936 · 2015 · External reference
Modelling a Silent Epidemic: A Review of the In Vitro Models of Latent Tuberculosis
10.3390/pathogens7040088 · 2018 · External reference
PhoP: A Missing Piece in the Intricate Puzzle of Mycobacterium tuberculosis Virulence
10.1371/journal.pone.0003496 · 2008 · External reference
Selectivity of TMC207 Towards Mycobacterial ATP Synthase Compared With That Towards the Eukaryotic Homologue
10.1128/aac.01393-08 · 2009 · External reference
Design of Novel Hybrid Thiourea–Phosphonate Derivatives as Potential Anti‐TMV Agents: In Silico Evaluation and (S, O)‐Pharmacophoric Site Identification
10.1002/jbt.70904 · 2026 · External reference
Mycobacterium tuberculosis F‐ATP Synthase Inhibitors and Targets
10.3390/antibiotics13121169 · 2024 · External reference
Targeting Mycobacterial F‐ATP Synthase C‐Terminal α Subunit Interaction Motif on Rotary Subunit γ
10.3390/antibiotics10121456 · 2021 · External reference
GPU‐Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions With Single‐pH Simulations
10.1021/acs.jcim.9b00754 · 2019 · External reference
Bioenergetic Inhibitors: Antibiotic Efficacy and Mechanisms of Action in Mycobacterium tuberculosis
10.3389/fcimb.2020.611683 · 2021 · External reference
10.1016/j.neuron.2018.08.011
10.1016/j.neuron.2018.08.011 · External reference
Bioenergetics of Mycobacterium: An Emerging Landscape for Drug Discovery
10.3390/pathogens7010024 · 2018 · External reference
Synthesis, Molecular Docking, and Anti‐Inflammatory Evaluation of Novel 4‐(Benzo [d][1, 3] Dioxol‐5‐Yloxy)‐N, N‐2‐yn‐1‐Amine Derivatives as Potent Cysteinyl Leukotriene Receptor (CysLT2) Antagonists
10.3897/pharmacia.72.e143171 · 2025 · External reference
Hypoxic Non‐Replicating Persistent Mycobacterium tuberculosis Develops Thickened Outer Layer That Helps in Restricting Rifampicin Entry
10.3389/fmicb.2019.02339 · 2019 · External reference
10.1101/2023.11.30.569372
10.1101/2023.11.30.569372 · External reference
Identification of 2‐Aryl‐Quinolone Inhibitors of Cytochrome Bd and Chemical Validation of Combination Strategies for Respiratory Inhibitors Against Mycobacterium tuberculosis
10.1021/acsinfecdis.2c00283 · 2023 · External reference
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Updated and Standardized Genome‐Scale Reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, Simulates Flux States Indicative of Physiological Conditions
10.1186/s12918-018-0557-y · 2018 · External reference
Optimizing Drug Discovery Using Multitasking Models for Quantitative Structure–Biological Effect Relationships: An Update of the Literature
10.1080/17460441.2023.2251385 · 2023 · External reference
Perturbation‐Theory Machine Learning for Multi‐Objective Antibacterial Discovery: Current Status and Future Perspectives
10.3390/app15031166 · 2025 · External reference
Computational Drug Repurposing for Antituberculosis Therapy: Discovery of Multi‐Strain Inhibitors
10.3390/antibiotics10081005 · 2021 · External reference
Binding Properties of the Anti‐TB Drugs Bedaquiline and TBAJ‐876 to a Mycobacterial F‐ATP Synthase
10.1016/j.crstbi.2022.09.001 · 2022 · External reference
Hierarchical Virtual Screening Approaches in Small Molecule Drug Discovery
10.1016/j.ymeth.2014.07.007 · 2015 · External reference
Heterogeneity in Tuberculosis Pathology, Microenvironments and Therapeutic Responses
10.1111/imr.12252 · 2015 · External reference
Structure of Mycobacterial NDH‐2 Bound to a 2‐Mercapto‐Quinazolinone Inhibitor
10.1021/acs.jmedchem.5c00049 · 2025 · External reference
Pharmacokinetics and Safety of TBAJ‐876, a Novel Antimycobacterial Diarylquinoline, in Healthy Subjects
10.1128/aac.00613-24 · 2024 · External reference
A Systematic Evaluation of Mycobacterium tuberculosis Genome‐Scale Metabolic Networks
10.1371/journal.pcbi.1007533 · 2020 · External reference
Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis
10.1371/journal.pcbi.1004543 · 2015 · External reference
Simulating Biomolecules With the Variable Protonation State: A Tutorial for Constant‐pH Molecular Dynamics in NAMD
10.1021/acs.jpcb.5c03069 · 2025 · External reference
10.1186/s13321‐024‐00855‐8
10.1186/s13321‐024‐00855‐8 · External reference
Target‐Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies
10.3390/biom12070878 · 2022 · External reference
Identification of Novel DNA Gyrase Inhibitor by Combined Pharmacophore Modeling, QSAR Analysis, Molecular Docking, Molecular Dynamics, ADMET and DFT Approaches
10.1016/j.actatropica.2024.107460 · 2024 · External reference
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Mycobacterial β‐Carbonic Anhydrases: Molecular Biology, Role in the Pathogenesis of Tuberculosis and Inhibition Studies
10.1016/bs.enz.2024.05.012 · 2024 · External reference
Force Field Limitations of All‐Atom Continuous Constant pH Molecular Dynamics
10.1021/acs.jpcb.4c05971 · 2024 · External reference
Structure of the NDH‐2–HQNO Inhibited Complex Provides Molecular Insight Into Quinone‐Binding Site Inhibitors
10.1016/j.bbabio.2018.03.014 · 2018 · External reference
The Role of Protonation States in Ligand‐Receptor Recognition and Binding
10.2174/1381612811319230004 · 2013 · External reference
3D Atom Based QSAR Model of DprE1 Inhibitors as Anti‐Tubercular Agents
10.52711/0974-360x.2021.01026 · 2021 · External reference
Lipidomics and Genomics of Mycobacterium tuberculosis Reveal Lineage‐Specific Trends in Mycolic Acid Biosynthesis
10.1002/mbo3.193 · 2014 · External reference
Structure of the Mycobacterial ATP Synthase Fo Rotor Ring in Complex With the Anti‐TB Drug Bedaquiline
10.1126/sciadv.1500106 · 2015 · External reference
Studying the Dynamics of the Drug Processing of Pyrazinamide in Mycobacterium tuberculosis
10.1371/journal.pone.0309352 · 2024 · External reference
Editorial Guidelines for Computational Studies of Ligand Binding Using MM/PBSA and MM/GBSA Approximations Wisely
10.1021/acs.jpcb.4c06614 · 2024 · External reference
The Enduring Hypoxic Response of Mycobacterium tuberculosis
10.1371/journal.pone.0001502 · 2008 · External reference
10.1128/cmr.00159‐19
10.1128/cmr.00159‐19 · External reference
Benchmarking Molecular Dynamics Force Fields for All‐Atom Simulations of Biological Condensates
10.1021/acs.jctc.3c00148 · 2023 · External reference
Structure‐Based Drug Design With Equivariant Diffusion Models
10.1038/s43588-024-00737-x · 2024 · External reference
Type‐II NADH Dehydrogenase (NDH‐2): A Promising Therapeutic Target for Antitubercular and Antibacterial Drug Discovery
10.1080/14728222.2017.1327577 · 2017 · External reference
10.26434/chemrxiv-2024-xt0rj
10.26434/chemrxiv-2024-xt0rj · External reference
Targeting Dormant Phenotype Acquired Mycobacteria Using Natural Products by Exploring Its Important Targets: In Vitro and In Silico Studies
10.3389/fcimb.2023.1111997 · 2023 · External reference
Bedaquiline‐ and Clofazimine‐Selected Mycobacterium tuberculosis Mutants: Further Insights on Resistance Driven Largely by Rv0678
10.1038/s41598-023-36955-y · 2023 · External reference
Simultaneous Modeling of Antimycobacterial Activities and ADMET Profiles: A Chemoinformatic Approach to Medicinal Chemistry
10.2174/15680266113139990116 · 2013 · External reference
In Silico Discovery and Virtual Screening of Multi‐Target Inhibitors for Proteins in Mycobacterium tuberculosis
10.2174/138620712802650487 · 2012 · External reference
New Insights Toward the Discovery of Antibacterial Agents: Multi‐Tasking QSBER Model for the Simultaneous Prediction of Anti‐Tuberculosis Activity and Toxicological Profiles of Drugs
10.1016/j.ejps.2013.01.011 · 2013 · External reference
Mycobacterium tuberculosis Responds to Chloride and pH as Synergistic Cues to the Immune Status of Its Host Cell
10.1371/journal.ppat.1003282 · 2013 · External reference
Recent Advances in Anti‐Tuberculosis Drug Discovery Based on Hydrazide–Hydrazone and Thiadiazole Derivatives Targeting InhA
10.3390/ph16040484 · 2023 · External reference
QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone‐Based Thiosemicarbazones Against Mycobacterium tuberculosis
10.3390/antibiotics12010061 · 2022 · External reference
DoGSiteScorer: A Web Server for Automatic Binding Site Prediction, Analysis and Druggability Assessment
10.1093/bioinformatics/bts310 · 2012 · External reference
Unresolved reference
2025 · External reference
Targeting Type II NADH Dehydrogenase in Tuberculosis Treatment: A Review
10.1016/j.ijbiomac.2025.143541 · 2025 · External reference
Structure of Mycobacterium tuberculosis Cytochrome Bcc in Complex With Q203 and TB47, Two Anti‐TB Drug Candidates
10.7554/elife.69418 · 2021 · External reference
