<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2022-05-19</periodOfReport>

    <dateOfOriginalSubmission>2022-05-23</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001662774</issuerCik>
        <issuerName>Cortexyme, Inc.</issuerName>
        <issuerTradingSymbol>CRTX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001929422</rptOwnerCik>
            <rptOwnerName>Hannah Brendan</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CORTEXYME, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>269 EAST GRAND AVE.</rptOwnerStreet2>
            <rptOwnerCity>SOUTH SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94080</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Business Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2022-05-19</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>113569</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>129793</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The shares vest monthly, subject to continued service.</footnote>
        <footnote id="F2">On March 19, 2022, the Issuer completed acquisition (the &quot;Merger&quot;) of Novosteo Inc. (&quot;Novosteo&quot;), pursuant to that certain Agreement and Plan of Merger and Reorganization, dated as of May 9, 2022, (the &quot;Merger Agreement&quot;), by and among the Issuer, Quince Merger Sub I, Inc., a wholly owned subsidiary of the Issuer, Quince Merger Sub II, LLC, a wholly owned subsidiary of the Issuer, Novosteo, and Fortis Advisors LLC, solely in its capacity as the securityholders' representative. Pursuant to the terms of the Merger Agreement, at the closing of the Merger, the shares held by the Reporting Person in Novosteo were automatically cancelled and converted into the right to receive shares of common stock of the Issuer.</footnote>
    </footnotes>

    <remarks>Due to an administrative error, the transaction reported in this Form 4 was inadvertently omitted from the original filing.  The total amount of shares owned is reported as of May 19, 2022.</remarks>

    <ownerSignature>
        <signatureName>/s/ Chris Lowe, Attorney-in-Fact for Brendan Hannah</signatureName>
        <signatureDate>2022-05-27</signatureDate>
    </ownerSignature>
</ownershipDocument>
