<p>SARS-CoV-2 has been exhibiting extremely spreading property all around the world since its existence from Wuhan-China in December-2019. Although it has caused a death toll of over than 1.3 M people, no validated vaccine has been proposed yet. On the other hand, very dense studies on the vaccine development have been carrying out in some countries such as the US, Germany, UK, China and Russia. Due to side effects of current antiviral agents used in the therapy of COVID-19, there is a great need for the development of alternative compounds for this disease. Caulerpin (CPN) and caulerpenyne (CYN), predominant natural secondary metabolites from invasive marine green algae <i>Caulerpa cylindracea,</i>are proposed to neutralize the virus from two targets: spike protein (5XLR) and main protease (6YB7) in this study. The results show that the binding energies related to CPN-6YB7 and CYN-6YB7 interactions are found to be -8.02 kcal/mol and -6.83 kcal/mol, respectively. The binding energies were -9.68 kcal/mol and -7.53 kcal/mol, respectively, for CPN-5XLR and CYN-5XLR. In the molecular dynamics results, RMSD values show that CPN and CYN can form stable complexes with the proteins where CYN is more stable with 6YB7 and CPN interacts better with 5XLR. These differences seem to be based on the type of interactions of the complexes. In conclusion, caulerpin and caulerpenyne can further be investigated experimentally for their anti-SARS-CoV-2 efficiency. </p>