Overall, I have published 7 articles, 1 review, 3 book chapters and 2 patent applications and these are my citation statistics from Google Scholar and my online mentions from Impactstory:

 

(last update April 2018) 

 

Original Research Articles                                                                                                              

 

Antolin AA, Tym JE, Komianou A, Collins I, Workman P and Al-Lazikani B

Objective, Quantitative, Data-Driven Assessment of Chemical Probes

Cell Chem Biol. 25, 194-205 (2018).
Citations: 3. IF: 5.6 Q1 Biochemistry & Molecular Biology

In this article we analyse the current landscape of chemical probes to study the human proteome and we describe the development of the Probe Miner online resource. Probe Miner uses public data available in the canSAR knowledgebase to objectively assess all publicly available compounds deposited in highly curated medicinal chemistry databases as chemical probes to study human targets. We strongly believe that given its breadth and ease to be updated, objective and data-driven assessment of chemical probes can highly complement more in depth expert assessment of chemical probes available at The Chemical Probes Portal and together contribute to address the current lack of data robustness and quality in biomedical research, particularly around the selection and use of chemical probes for target validation. A press release was issued by The Institute of Cancer Research and a post at Prof. Workman blog 'The Drug Discoverer' regarding Probe Miner. Our article attracted the attention of several magazines and online news websites such as The Scientist and Laboratory News and MedChemNet have commissioned editorials on Probe Miner. We hope Probe Miner will be a valuable tool for the community to help in the assessment and selection of chemical probes.

 

Tym JE†, Mitsopoulos C†, Coker EA, Razaz P, Schierz AC, Antolin AA and Al-Lazikani B

canSAR: an updated cancer research and drug discovery knowledgebase

Nucleic Acids Res.. 42(Database issue), D1040-7 (2016).
 Citations: 29. IF: 9.112. Q1 D1 Biochemistry & Molecular Biology

In this updated version of the multidisciplinary, cancer-focused knowledgebase canSAR developed to support cancer translational research and drug discovery and published in the prestigious database issue of NAR we include major enhancements to canSAR such as new data, improved search and browsing capabilities, new disease and cancer cell line summaries and new and enhanced batch analysis tools. Moreover, I have participated by curating information on Chemical Probes from several resources to help scientists choose the best chemical probes to validate their targets and thus contribute to solve the problems with target validation and data reproducibility that we face in modern drug discovery and translational research. The database was highlighted in the Lancet Oncology. We continue to work to improve the access to the information regarding chemical probes that is available in canSAR. Hopefully, more updates soon!

 

Rubio-Perez C*, Tamborero D*, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N.

In silico prescription of anti-cancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities

Cancer Cell. 27, 382-396 (2015).
                         Citations: 137. IF: 23.893. Q1 D1 Oncology

In this work we collaborated with Nuria Lopez-Bigas' Biomedical Genomics group also in the GRIB to identify the driver genes of a large pan-cancer cohort of tumors and then access the scope of targeted agents in this cohort. Nicely, we showed that despite only 6% of tumor are tractable by approved drugs following clinical guidelines, 40% of patients could benefit from repurposing of approved drugs, illustrating the importance of analyzing each tumor's aberrations and the necessary transition towards precision oncology. Interestingly also many drugs' polypharmacology could be exploited better in precision cancer medicine since we found cases in which a drug inhibits several drivers at the same time. Hopefully we will expand these cases in the future as we identify new targets of drugs but cancer medicine has yet to find a way to make the most of it. Unfortunately, many sub-clonal lowly-recurrent cancer drivers were also identified in line of recent reports predicting that the number of these drivers will increase in the future as we deepen our sequencing efforts. As a comprehensive drug arsenal covering all drivers seems increasingly unlikely, we must find innovative ways in drug discovery to counteract lowly-recurrent cancer drivers and their role in drug resistance. This article was highlighted in Nature Reviews Drug Discovery, Cancer Discovery and Science Translational Medicine.

 

A. A. Antolin, J. Mestres.

  Distant polypharmacology among MLP chemical probes

ACS Chemical Biology. 10, 395-400 (2015).
Citations: 15. IF: 5.356. Q1 D2 Biochemistry & Molecular Biology

 

This publication nicely exemplifies one of the main conclusions of my PhD Thesis: chemical probes, as well as drugs, show widespread polypharmacology and their off-targets can be phylogenetically unrelated to their primary target. This important discovery was highlighted as cover of the February 2015 ACS Chemical Biology issue showing our astronomic analogy entitled "Uncovering the Target Space of Chemical Probes". Hopefully, this publication will raise awareness in the chemical probe community about the ubiquity of polypharmacology and the importance of considering it while using and developing chemical probes. Moreover, this work illustrates the capacity of in silico target profiling methods to de-risk the practice of chemical biology as we advance towards precision medicine.

 

 

A. A. Antolín, J. Mestres.

Linking off-target kinase pharmacology to the differential cellular effects observed among PARP inhibitors

                         Oncotarget. 5, 3023-8 (2014).
                         Citations: 24. IF: 6.636. Q1 D1 Oncology

 

In this article the trail of chemical probe polypharmacology uncovered in my first publication lead us to uncover that PARP drugs in clincal trials have different micromolar affinity for a pannel of 16 kinases selected using a computational approach that relates proteins by their shared ligands. Moreover, we link these in vitro off-target effects to the different cellular effects of PARP inhibitors that continue being uncovered and we warn the wide scientific community of both the oportunities that these new afinities offer to widen the patient population that could benefit from each PARP inhibitor and of the risks of translating pre-clinical and clinical outcomes from one PARP inhibitor to another. PARP inhibitors seem to have a natual tendency to inhibit kinases and each PARP drug candidate needs to be thus considered as a unique entity. More recently, this work has also lead to the introduction of kinase panels to test the selectivity of newly developed PARP inhibitors NMS-P118 against kinases.

 

 

A. A. Antolín, A. Carotti, R. Nuti, A. Hakkaya, E. Camaioni, J. Mestres, R. Pellicciari and A. Macchiarulo.

Exploring the effect of PARP-1 flexibility in docking studies

J Mol Graph Model. 45, 192-201 (2013).
Citations: 8. IF: 2.325. Q1 D2 Computer Science, Interdisciplinary Applications

 

This Article includes the work I performed at the university of Perugia (Italy) under the direction of Dr. Macchiarulo at the Pellicciari Group. Using REMD we studied the dynamic properties of PARP-1, we demonstrated that the use of REMD ensambles improves docking results and we discovered a new pocket that might be important to explain the binding of some lingands into PARP-1.

 

 

 A. A. Antolín, X. Jalencas, J. Yelamos and J. Mestres.

Identification of Pim Kinases as Novel Targets for PJ34 with Confounding Effects in PARP Biology

ACS Chem Biol. 7, 1962-7 (2012).
Citations: 49. IF: 6.446. Q1 D2 Biochemistry & Molecular Biology

 

In this letter we use the software developed at the lab PredictFX to predict and then we validate in vitro that PJ34, a chemical probe widely used to study PARP-1 biology, binds to Pim1 and Pim2 kinases with micromolar affinity. Pim kinases are able to explain many of the PARP-1 independent effects of PJ34, however, the difference in affinity between PARP-1 and Pim1 is sufficinetly high to safely use PJ34 to probe for PARPs. However, PJ34 is used routinely at very high concentrations, where confounding effects due to Pim1 inhibition can occur. As an example, it has recently been demonstrated that PARP-1 is really not involved in TNF-necroptosis, despite during 10 years it was believed that both targets were acting on the same pathway because of the wrong use of a chemical probe. Take home messages: Use PJ34 at concentrations lower that 1micromolar, always use more than one chemical probe if possible and at the lower concentration possible.

 

 

Reviews                                                                                                                                           

 

A. A. Antolín, P. Workman, J. Mestres and B. Al-Lazikani.

Polypharmacology in Precision Oncology: Current Applications and Future Prospects

Curr Pharm Des. 22, 6935-6945 (2016).
Citations: 8. IF: 2.611. Q2

 

In this review we analyzed the FDA list of approved pharmacogenomic biomarkers to identify the cases where a cancer drug has been approved in more than one oncology indication thanks to its binding to more than one target. Both imatinib and crizotinib illustrate how polypharmacology is already being exploited in cancer precision oncology. However, we also discuss the challenges, limitations and future prospects en route towards fully identifying and exploiting drug polypharmacology for the benefit of cancer patients.

 

Patents                                                                                                                                            

 

                                    LABORATORIOS SALVAT, S.A.

CATENA RUIZ, Juan Lorenzo; SERRA COMAS, Carme; REY PUIGGROS, Oscar;

ANTOLIN HERNANDEZ, Albert; MONLLEO MAS, Ester

Inhibitor compounds of 11-beta-Hydroxysteroid dehydrogenase type 1

WO/2010/139827

 

 

                 Fundació Institut Mar d’Investigacio Medica, Barcelona (ES)

PEIRO SALES, Sandra; MESTRES LOPEZ, Jordi; CEBRIA COSTA, Joan Pau;

ITURBIDE MARTÍNEZ DE ALBÉNIZ, Ane; ANTOLIN HERNANDEZ, Albert

Zonisamide for use in the treatment of breast cancer

                       EP3241562 (A1)

 

 

Book chapters                                                                                                                              


A. A. Antolín, J. Mestres.

The polypharmacology gap between

chemical biology and drug discovery.

In "Computational Tools for Chemical Biology". Sonsoles Martin-Santamaria (Eds).
Royal Society of Chemistry 2018.

               Link to Book

 

In this bookchapter we highlight the importance of in silico target profiling as a computational tool to de-risk the use of chemical probes with unknown off-targets that might confound the observed effects by illustrating the effects it had for understanding PARP biology and developing PARP drugs.

 

 A. A. Antolín, J. Mestres.

The impact of distant polypharmacology in the

chemical biology of PARPs.

In "Concepts and Case Studies in Chemical Biology". H Waldmann and P. Janning (Eds).
Wiley-VCH, Weinheim 2014.

                       Link to Book

 

In this educational bookchapter primarly directed to Master Students of Chemical Biology we summarize many of the conclusions of my PhD for the practise of Chemical Biology by explaining the case of PJ34. In brief, chemical probes tend to be polypharmacological, their use at high concentrations increases the risk of confounding effects and the fact that the target profile of a chemical probe is unknown affects the development of drugs inspired on this chemical probe. Fortunately, we have now computational methods that help us to unrabel the confounding off-targets of chemical probes at a reduced cost. Please, do use them!

 

 A. A. Antolín, J. Mestres.

Knowledge Base for Nuclear Receptor Drug Discovery

In "Therapeutic Targets: Modulation, Inhibition, and Activation". L. M. Botana and M. Loza (Eds).
John Wiley & Sons, New Jersey 2012. Citations: 2.

Link to Book

In this bookchapter we collect and analyze all the information availiable on Nuclar Receptors. It's interesting to aknowledge how drug polypharmacology arises in this target family, both between proteins of the same family and between distantly related proteins.

 

 

PhD Thesis                                                                                                                                  


A. A. Antolin

Thesis director: Dr. J. Mestres

The impact of polypharmacology on chemical biology

Defended October 9th 2014, excellent cum laude

                       European PhD Mention and Extraordinary Prize

 

 

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