Publications

  • RELEVANT PUBLICATIONS

Mendoza-Salazar, I., Fragozo, A., González-Martínez, A. P., Trejo-Martínez, I., Arreola, R., Pavón, L., Almagro, J. C., Vallejo-Castillo, L., Aguilar-Alonso, F. A., & Pérez-Tapia, S. M. Almost 50 Years of Monomeric Extracellular Ubiquitin (eUb). Pharmaceuticals, 17(2), 185, 2024.  

Maciuba S, Bowden GD, Stratton HJ, Wisniewski K, Schteingart CD, Almagro JC, Valadon P, Lowitz J, Glaser SM, Lee G, Dolatyari M, Navratilova E, Porreca F, Rivière PJM. Discovery and characterization of prolactin neutralizing monoclonal antibodies for the treatment of female pain. mAbs. 15:  2254676, 2023. 

Godínez-Palma S, González-González E, Ramírez-Villedas F, Garzón-Guzmán C, Vallejo-Castillo L, Carballo-Uicab G, Marcelín-Jiménez Gabriel, Batista D, Pérez-Tapia SM, Almagro JC. Efficacy, pharmacokinetic and toxicity profiles of a broadly SARS-CoV2 neutralizing antibody. Viruses. 15: 1733. 2023.

Daniels-Wells TR, Pierre V. Candelaria PV, Kranz E, Wen J, Wang L, Kamata M, Almagro JC, Martínez-Maza O, Penichet ML. Efficacy of antibodies targeting transferrin receptor 1 in xenograft mouse models of AIDS-related non-Hodgkin lymphoma. Cancers. 15: 1816. 2023.

Guzmán-Bringas OU, Gómez-Castellano K, González-González E, Salinas-Trujano J, Vázquez-Leyva S, Vallejo-Castillo L, Pérez-Tapia SM, Almagro JC. Discovery and optimization of neutralizing SARS-CoV-2 antibodies using ALTHEA Gold Plus Libraries™. Int. J. Mol. Sci. 24: 4609. 2023.

González-González E, Carballo-Uicab G, Juana Salinas-Trujano J, María I. Cortés-Paniagua MI, Said Vázquez-Leyva S, Vallejo-Castillo L, Mendoza-Salazar I, Gómez-Castellano K, Pérez-Tapia SM, Almagro JC. In vitro and in vivo characterization of a broadly neutralizing anti-SARS-CoV-2 antibody isolated from a semi-immune phage display library. Antibodies. Antibodies (Basel). 11: 57. 2022.

Almagro JC, Mellado-Sánchez G, Pedraza-Escalona M, Pérez-Tapia SM. Evolution of approved anti-SARS-COV-2 therapeutic antibodies. Int. J. Mol. Sci. 23: 9763. 2022.

• Invited Review

Mendoza-Salazar I, Gómez-Castellano KM, González-González E, Gamboa-Suasnavart R, Rodríguez-Luna SD, Santiago-Casas G, Cortés-Paniagua MIC, Pérez-Tapia SM, Almagro JC. Anti-SARS-CoV-2 Omicron antibodies isolated from a SARS-CoV-2 Delta semi-immune phage display library. Antibodies (Basel). 11: 13. 2022.

Pedraza-Escalona M, Guzmán-Bringas O, Arrieta-Oliva I, Gómez-Castellano K, Salinas-Trujano J, Torres-Flores J, Muñoz-Herrera JC, Camacho-Sandoval R, Contreras-Pineda P, Chacón-Salinas R, Pérez-Tapia SM, Almagro JC. Isolation and characterization of high affinity and highly stable anti-Chikungunya virus antibodies using ALTHEA Gold Libraries™. BMC Infectious Diseases. 21: 1121, 2021.

Camacho-Sandoval R, Nieto-Patlán A, Carballo-Uicab G; Montes A, Jiménez-Martínez MC, Vallejo-Castillo L, González-González E; Arrieta-Oliva HI, Gómez-Castellano K, Guzman-Bringas U, Cruz-Domínguez MP, Medina G, Montiel-Cervantes LA, Pérez-Tapia SM, Almagro JC. Development and Evaluation of a Set of Spike and Receptor Binding Domain-Based Enzyme-Linked Immunosorbent Assays for SARS-CoV-2 Serological Testing. Diagnostics. 11: 1506, 2021. 

Almagro JC, Pedraza M, Arrieta HI, Pérez-Tapia SM. Phage Display Libraries for Antibody Therapeutic Discovery and Development. Antibodies. 8: 44, 2019.

• Invited Review

Valadon P, Pérez-Tapia SM, Nelson RS, Guzmán-Bringas OU, Arrieta-Oliva HI, Gómez-Castellano KM, Pohl MA, Almagro JC. ALTHEA Gold Libraries™: Antibody Libraries for Therapeutic Antibody Discovery. MAbs. 11: 516-531, 2019.  

Almagro JC, Daniels-Wells TR, Perez-Tapia SM, Penichet ML. Progress and challenges in the design and clinical development of antibodies for cancer therapy. Frontiers in Immunology. 8: 1751-1770, 2018. 

• Invited Review

Teplyakov A, Obmolova G, Malia TJ, Raghunathan G, Martinez C, Fransson J, Edwards W, Connor J, Husovsky M, Beck H, Chi E, Fenton S, Zhou H, Almagro JC, Gilliland GL. Structural insights into humanization of anti-tissue factor antibody 10H10. MAbs. 10: 269-277, 2018.

Teplyakov A, Obmolova G, Malia TJ, Luo J, Muzammil M, Sweet RW, Almagro JC,  Gilliland GL. Structural Diversity in a Human Antibody Germline Library. MAbs. 21: 1-19, 2016.

Almagro JC, Teplyakov A, Luo J, Sweet RW, Kodangattil S, Hernadez-Guzman F, Stanfield R, Gilliland GL. Second Antibody Modeling Assessment (AMA-II). Proteins. 82: 1553-1562, 2014.

Teplyakov A, Luo J, Obmolova G, Malia TJ, Sweet R, Stanfield RL, Kodangattil S, Almagro JC, Gilliland GL. Antibody Modeling Assessment II: Structures and Models. Proteins. 82: 1563-1582, 2014.

Malia TJ, Teplyakov A, Brezski RJ, Luo J, Kinder M, Sweet RW, Almagro JC, Jordan RE, Gilliland GL. Structure and Specificity of an Antibody Targeting a Proteolytically-cleaved IgG Hinge. Proteins. 82: 1656-1667, 2014.

Kodangattil S, Huard C, Ross C, Li J, Gao H, Mascioni A, Hodawadekar S, Naik S, Visintin A, Almagro JC. The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing.  mAbs. 30: 628-636, 2014.

Almagro JC, Gilliland GL, Breden F, Scott J, Sok D, Pauthner M, Reichert JM, Helguera G, Andrabi R, Mabry R, Bléry M, Voss JE, Laurén J, Abuqayyas L, Barghorn S, Ben-Jacob E, Crowe JE, Huston JS, Johnston SA, Krauland E, Lund-Johansen F, Marasco WA, Parren PWHI, Xu KY. Antibody Engineering and Therapeutics: December 8-12, 2013, Huntington Beach, CA. mAbs.  6: 577-618, 2014.

Almagro JC, Gilliland GL., Scott JK, Larrick JW., Plückthun A, Veldman T, Adams GP, Parren PWHI., Bradbury A, Reichert J M, Huston JS. Antibody Engineering & Therapeutics Conference, the Annual Meeting of The Antibody Society, December 8-12, 2013, Huntington Beach CA. mAbs. 5: 1-9, 2013.

Finlay WJJ and Almagro JC. Natural and Man-made V-region repertoires for Antibody Discovery. Frontiers in Immunology. 3: 1-18, 2012.  


• Invited Review 

Canziani G, Nemeth JF, Sweet R, Scallon B and Almagro JC, Knight D and Gilliland GL. Biologics and molecular recognition: Mike Brigham-Burke memorial issue.  J. Mol. Recognit. 25: 99-102, 2012.

Raghunathan G, Smart J, Williams JJ and Almagro JC. Antigen-Binding Site Anatomy and Somatic Mutations of Antibodies that Recognize Different Types of Antigens. J. Mol. Recognit. 25: 103-113, 2012. 

Almagro JC, Raghunathan G, Beil E, Janecki DJ, Qiang C, Dinh T, LaCombe A, Connor J, Ware M, Kim PH, Teplyakov A, Swanson RV and Fransson J. Characterization of a high affinity human antibody with a disulfide bond in CDR-H3. J. Mol. Recognit. 25: 125-135, 2012.

Gilliland GL, Luo J, Vafa O and Almagro JC. Leveraging SBDD in protein therapeutic development: antibody engineering. Methods in Molecular Biology. 841: 321-349, 2012. 


• Invited Review 

Almagro JC, Beavers MP, Hernandez-Guzman F, Shaulsky J, Butenhof K, Maier J, Kelly K, Labute P, Thorsteinson N, Teplyakov A, Luo J, Sweet R and Gilliland GL. Antibody Modeling Assessment. Proteins. 79: 3050-3066, 2011.

Malia TJ, Obmolova G, Almagro JC, Gilliland GL and Teplyakov A. Crystal structure of human germline antibody 3-23/B3. Mol. Immunol. 248: 1586-1588, 2011.

Fransson J, Teplyakov A, Raghunathan G, Chen J, Cordier W, Dinh T, Lollo B,  Nishioka W, Zhou M, Feng Y, Chi E, Swanson R, Gilliland G and Almagro JC. Human Framework Adaptation of a mouse anti-IL13-neutralizing antibody. J. Mol. Biol. 398: 214-231, 2010.

Shi L, Wheeler JC, Sweet RW, Lu J, Luo J, Tornetta M, Whitaker B, Reddy R, Brittingham R,  Borozdina L, Chen Q, Amegadzie B, Knight DM, Almagro JC and Tsui P. De novo selection of high affinity antibodies from synthetic Fab libraries displayed on phage as pIX-fusion proteins. J. Mol. Biol. 387: 385-396, 2010.

Cobaugh CW, Almagro JC, Pogson M, Iverson B, Georgiou G. Synthetic antibody libraries with a bias towards peptide ligands. J. Mol. Biol. 378: 622-33, 2008.   

• Nominated for Faculty of 1000 Biology, July 2008   

Almagro JC, Fransson J. Humanization of antibodies. Frontier in Biosciences. 13:1619-1633, 2008. 

• Invited Review 

• Published in The Encyclopedia of Biosciences. 

Gomez I, Arenas I, Benitez I, Miranda-Rios J, Becerril B, Grande R, Almagro JC, Bravo A, Soberon M. Specific epitopes of domains II and III of bacillus thuringiensis Cry1Ab toxin involved in the sequential interaction with cadherin and aminopeptidase-N receptors in manduca sexta. J. Biol. Chem. 281: 34032-34039, 2006.

Almagro JC, Quintero V, Ortiz M, Velandia A, Smith SL, Becerril B. High affinity antibodies isolated from a synthetic VH repertoire with tailored diversity for recognition of protein and peptides. J. Mol. Recognit. 19: 413-422, 2006.

Almagro JC, Martinez L, Smith SL, Alagon A, Paniagua J, Estevez J. Analysis of the horse VH repertoire and comparison with the human IGHV germline genes, and sheep, cattle and pig VH sequences. Mol. Immunol. 43: 1836-1845, 2006.

Hwang WY, Almagro JC, Buss TN, Tan P, Foote J. Use of human germline genes in a CDR homology-based approach to CDR grafting. Methods. 36: 35-42, 2005. 

Almagro JC. Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires. J. Mol. Recognit. 17: 132-143, 2004. 

Martinez L, Almagro JC, Coll JL, Herrera RJ. Sequence variability in the Fibroin-H Intron of domesticated and wild silk moths. Insect. Biochem. Mol. Biol. 34: 343-352, 2004.

Rojas G, Almagro JC, Acevedo B, Gavilondo JV. Phage antibody fragments library combining a single human light chain variable region with immune mouse heavy chain variable regions. J. Biotechnol. 94: 287-298, 2002. 

Ramirez-Benitez M del C, Moreno-Hagelsieb G, Almagro JC. VIR.II: a new interface with the antibody sequences in the Kabat database. Biosystems. 61: 125-131, 2001.

Ramirez-Benitez MC, Almagro JC. Analysis of antibodies of known structure suggests a lack of correspondence between residues in contact with the antigens and those modified by somatic hypermutation. Proteins. 45: 199-206, 2001. 

Manoutcharian K, Gevorkian G, Cano A, Almagro JC. Phage displayed biomolecules as preventive and therapeutic agents. Curr. Pharm. Biotechnol. 2: 217-223, 2001.

Vorobjev Y, Almagro JC, Hermans J. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins. 32: 399-413, 1998. 

Gevorkian G, Manoutcharian K, Almagro JC, Govezensky T, Dominguez V. Identification of autoimmune thrombocytopenic purpura-related epitopes using phage-display peptide library. Clin. Immunol. Immunopatol. 86: 305-309, 1998.

Almagro JC, Hernandez I, Ramirez-Benitez MC, Vargas-Madrazo E. The structural differences between the repertoire of Igk-V germline genes of mouse and human and their evolutionary implications. Immunogenetics. 47: 355-363, 1998. 

Almagro JC, Hernandez I, Ramirez-Benitez MC, Vargas-Madrazo E. The differences between the structural repertoires of VH germ-line gene segments of mice and humans: implication for the molecular mechanism of the immune response. Mol. Immunol. 34: 1199-1214, 1997. 

Vargas-Madrazo E, Lara-Ochoa F, Ramirez-Benitez MC, Almagro JC. Evolution of the structural repertoire of the human VH and Vk germline genes. Int. Immunol. 9: 1801-1815, 1997. 

Lara-Ochoa F, Almagro JC, Vargas-Madrazo E, Conrad M. Antigen-antibody recognition: a canonical structure paradigm. J. Mol. Evol. 43: 678-684, 1996.

Gevorkian G, Manoutcharian K, Larralde C, Hernadez M, Almagro JC, Viveros M, Sotelo J, Garcia E, Sciutto E. Immunodominant synthetic peptides of Taenia crassiceps in murine and human cysticercosis. Immunological Letters. 49: 185-189, 1996. 

Lara-Ochoa F, Almagro JC, Vargas-Madrazo E, Mendez I. Frequencies analysis of amino acids in the recognition regions of T-cell receptors. Biosystems. 39: 77-86, 1996.

Almagro JC, Lara-Ochoa F, Vargas-Madrazo E. Structural repertoire in human VL pseudogenes of immunoglobulins: comparison with functional germline genes and amino acids sequences. Immunogenetics. 43: 92-96, 1996.

Vargas-Madrazo E, Lara-Ochoa F, Almagro JC. Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition. J. Mol. Biol. 254: 497-504, 1995.

Almagro JC, Vargas-Madrazo E, Lara-Ochoa F, Horjales E. Molecular modeling of a T-cell receptor bound to a major histocompatibility complex molecule: implications for the T-cell recognition. Protein Sci. 4:1708-1717, 1995.

Vargas-Madrazo E, Almagro JC, Lara-Ochoa F. Structural repertoire in VH pseudogenes of immunoglobulins: comparison with human germline genes and human functional sequences. J. Mol. Biol. 246: 74-81, 1995. 

Lara-Ochoa F, Vargas-Madrazo E, Almagro JC. Distribution of the use frequencies of amino acids in the hypervariable regions of immunoglobulins. J. Mol. Evol. 41: 98-103, 1995. 

Almagro JC, Zenteno R, Vargas-Madrazo E, Lara-Ochoa F. Variability analysis of the T-cell receptors using three variability indexes. Inter. J. Protein & Peptide Res. 45:180-186, 1995. 

Almagro JC, Lara-Ochoa F, Zenteno-Cuevas R, Hernandez-Mendiola V, Vargas-Madrazo E. VIR: a computational tool for analysis of the variable domains of immunoglobulin sequences. BioSystems. 35: 25-32, 1995.

Lara-Ochoa F, Vargas-Madrazo E, Jiménez-Montaño MA, Almagro JC. Patterns in the complementary determining regions of immunoglobulins (CDRs). BioSystems. 32:1-9, 1994.