A Combinatorial Computational Approach for Drug Discovery Against AIDS: Machine Learning and Proteochemometrics

Computational methods have been widely used in drug discovery including identification of novel targets, studying drug target interactions, and in virtual screening of compounds against known targets. Machine learning techniques have been used in predictions of novel targets and drugs with greater accuracy compared to other methods. Machine learning algorithms have also been widely used in predicting the progression of disease, resistance of a drug to a virus, treatment efficacy prediction, and also in predicting the effectiveness of combinational therapy with respect to HIV-1. In this article, we have focused on some of the machine learning techniques in the context of viral disease. In brief, machine learning methods have great potential in drug discovery, drug repurposing, and in precision medicine.

[1]  Y. Singh Machine Learning to Improve the Effectiveness of ANRS in Predicting HIV Drug Resistance , 2017, Healthcare informatics research.

[2]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[3]  Jean-Philippe Vert,et al.  Virtual screening of GPCRs: An in silico chemogenomics approach , 2008, BMC Bioinformatics.

[4]  Ola Spjuth,et al.  Proteochemometric Modeling of the Susceptibility of Mutated Variants of the HIV-1 Virus to Reverse Transcriptase Inhibitors , 2010, PloS one.

[5]  Vladimir N. Vapnik,et al.  The Nature of Statistical Learning Theory , 2000, Statistics for Engineering and Information Science.

[6]  Ron Kohavi,et al.  Wrappers for Feature Subset Selection , 1997, Artif. Intell..

[7]  Tin Kam Ho,et al.  The Random Subspace Method for Constructing Decision Forests , 1998, IEEE Trans. Pattern Anal. Mach. Intell..

[8]  Peteris Prusis,et al.  Proteochemometric modeling of HIV protease susceptibility , 2008, BMC Bioinformatics.

[9]  P. Harrigan,et al.  Baseline HIV drug resistance profile predicts response to ritonavir-saquinavir protease inhibitor therapy in a community setting. , 1999, AIDS.

[10]  Leo Breiman,et al.  Classification and Regression Trees , 1984 .

[11]  B. Clotet,et al.  Classification Models for Neurocognitive Impairment in HIV Infection Based on Demographic and Clinical Variables , 2014, PloS one.

[12]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..

[13]  Kilian Q. Weinberger,et al.  Distance Metric Learning for Large Margin Nearest Neighbor Classification , 2005, NIPS.

[14]  Thomas Lengauer,et al.  Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Vladimir Vapnik,et al.  Statistical learning theory , 1998 .

[16]  Kilian Stoffel,et al.  Theoretical Comparison between the Gini Index and Information Gain Criteria , 2004, Annals of Mathematics and Artificial Intelligence.

[17]  Irene T. Weber,et al.  Automated prediction of HIV drug resistance from genotype data , 2016, BMC Bioinformatics.

[18]  R. Shafer Rationale and uses of a public HIV drug-resistance database. , 2006, The Journal of infectious diseases.

[19]  Sorin Draghici,et al.  Predicting HIV drug resistance with neural networks , 2003, Bioinform..

[20]  Zhiwei Cao,et al.  Proteochemometric Modeling of the Bioactivity Spectra of HIV-1 Protease Inhibitors by Introducing Protein-Ligand Interaction Fingerprint , 2012, PloS one.

[21]  V. Poroikov,et al.  A Computational Approach for the Prediction of HIV Resistance Based on Amino Acid and Nucleotide Descriptors , 2018, Molecules.

[22]  B. Schmidt,et al.  Phenotypic HIV-1 Resistance Correlates with Treatment Outcome of Nelfinavir Salvage Therapy , 1999, Antiviral therapy.

[23]  S. Hensley,et al.  A comprehensive archaeological map of the world's largest preindustrial settlement complex at Angkor, Cambodia , 2007, Proceedings of the National Academy of Sciences.

[24]  JD Lundgren,et al.  Updated European Recommendations for the Clinical Use of HIV Drug Resistance Testing , 2004, Antiviral therapy.

[25]  P. Reiss,et al.  HIV-1 infection and cognitive impairment in the cART era: a review. , 2011, AIDS.

[26]  Amir Assadi,et al.  Unsupervised clustering algorithm for N-dimensional data , 2005, Journal of Neuroscience Methods.

[27]  P. Volberding,et al.  Novel four-drug salvage treatment regimens after failure of a human immunodeficiency virus type 1 protease inhibitor-containing regimen: antiviral activity and correlation of baseline phenotypic drug susceptibility with virologic outcome. , 1999, The Journal of infectious diseases.

[28]  M. Mars,et al.  Support vector machines to forecast changes in CD4 count of HIV-1 positive patients. , 2010 .

[29]  S. Hammer,et al.  Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. , 2008, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[30]  X. Chen,et al.  TTD: Therapeutic Target Database , 2002, Nucleic Acids Res..

[31]  John B. O. Mitchell,et al.  A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking , 2010, Bioinform..

[32]  B. Rapkin,et al.  Classification and regression tree uncovered hierarchy of psychosocial determinants underlying quality-of-life response shift in HIV/AIDS. , 2009, Journal of clinical epidemiology.

[33]  Lorenzo Bruzzone,et al.  Kernel-based methods for hyperspectral image classification , 2005, IEEE Transactions on Geoscience and Remote Sensing.

[34]  Gerard J. P. van Westen,et al.  Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data , 2013, PLoS Comput. Biol..

[35]  Robert P. Sheridan,et al.  Random Forest: A Classification and Regression Tool for Compound Classification and QSAR Modeling , 2003, J. Chem. Inf. Comput. Sci..

[36]  A. Wensing,et al.  Computational models can predict response to HIV therapy without a genotype and may reduce treatment failure in different resource-limited settings. , 2013, The Journal of antimicrobial chemotherapy.

[37]  C. Hansch Quantitative approach to biochemical structure-activity relationships , 1969 .

[38]  P. Garg,et al.  An improved approach for predicting drug-target interaction: proteochemometrics to molecular docking. , 2016, Molecular bioSystems.

[39]  Michael I. Jordan,et al.  Machine learning: Trends, perspectives, and prospects , 2015, Science.

[40]  Barbara Schmidt,et al.  Simple algorithm derived from a geno-/phenotypic database to predict HIV-1 protease inhibitor resistance , 2000, AIDS.

[41]  Cynthia Brandt,et al.  Semi-supervised clinical text classification with Laplacian SVMs: An application to cancer case management , 2013, J. Biomed. Informatics.

[42]  Brendan Larder,et al.  A Comparison of Three Computational Modelling Methods for the Prediction of Virological Response to Combination Hiv Therapy Author's Personal Copy , 2022 .

[43]  Jarl E. S. Wikberg,et al.  Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors , 2009, J. Chem. Inf. Model..

[44]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.