This book is focused on molecular modeling using both structure based and ligand based design followed by synthesis of potential anticancer agents. Heat shock protein 90 and Cyclin dependent kinase 1 are used as a valid target for developing anticancer agents. Cyclin dependent kinase-1 (CDK1) and heat shock protein 90 (HSP90) were explored by molecular modeling towards the discovery of new dual inhibitors with potential anticancer properties. Both targets are critical for cancer progression and metastasis. In fact, CDK1 is considered as one of the natural substrates for HSP90, therefore, dual inhibition is expected to effectively arrest tumor growth, development and metastasis. The modeling studies were conducted employing structure-based (chapters 3, 4) and ligand-based methodologies (chapters 1, 2). Several new compounds were found to inhibit CDK1 (chapter 1) or HSP90, albeit selectively. Thiamine was found to possess good anti-HSP90 properties, and therefore was employed as lead for subsequent optimization of better HSP90 inhibitors based on pyridinium derivatives (chapter 5).